diff --git a/docs/_images/parakeet_logo.png b/docs/_images/parakeet_logo.png new file mode 100644 index 00000000..eb6a080a Binary files /dev/null and b/docs/_images/parakeet_logo.png differ diff --git a/docs/_sources/api.rst.txt b/docs/_sources/api.rst.txt new file mode 100644 index 00000000..b0f471a5 --- /dev/null +++ b/docs/_sources/api.rst.txt @@ -0,0 +1,98 @@ +Python API +========== + +.. warning:: This is under developement + +The functionality of the command line programs can be called from python as shown below. + +Image IO functions +------------------ + +.. autofunction:: parakeet.io.new + +.. autofunction:: parakeet.io.open + +PDB file functions +------------------ + +.. autofunction:: parakeet.data.get_pdb + +Configuration functions +----------------------- + +.. autofunction:: parakeet.config.new + +Sample functions +---------------- + +.. autofunction:: parakeet.sample.new + +.. autofunction:: parakeet.sample.add_molecules + +.. autofunction:: parakeet.sample.mill + +.. autofunction:: parakeet.sample.sputter + +Image simulation functions +-------------------------- + +.. autofunction:: parakeet.simulate.potential + +.. autofunction:: parakeet.simulate.exit_wave + +.. autofunction:: parakeet.simulate.optics + +.. autofunction:: parakeet.simulate.image + +.. autofunction:: parakeet.simulate.ctf + +Analysis functions +------------------ + +.. autofunction:: parakeet.analyse.correct + +.. autofunction:: parakeet.analyse.reconstruct + +.. autofunction:: parakeet.analyse.average_particles + +.. autofunction:: parakeet.analyse.average_all_particles + +.. autofunction:: parakeet.analyse.extract + +.. autofunction:: parakeet.analyse.refine + +.. autofunction:: parakeet.run + + +Data models +----------- + +.. autoclass:: parakeet.beam.Beam + :members: + + .. automethod:: __init__ + +.. autoclass:: parakeet.detector.Detector + :members: + + .. automethod:: __init__ + +.. autoclass:: parakeet.lens.Lens + :members: + + .. automethod:: __init__ + +.. autoclass:: parakeet.microscope.Microscope + :members: + + .. automethod:: __init__ + +.. autoclass:: parakeet.scan.Scan + :members: + + .. automethod:: __init__ + +.. autoclass:: parakeet.sample.Sample + :members: + + .. automethod:: __init__ diff --git a/docs/_sources/configuration.rst.txt b/docs/_sources/configuration.rst.txt new file mode 100644 index 00000000..ce90f152 --- /dev/null +++ b/docs/_sources/configuration.rst.txt @@ -0,0 +1,234 @@ +Configuration +============= + +Definitions +----------- + +Parakeet is configured via a YAML configuration file. The parameters of the +configuration file are defined below and additional example configuation files +can be seen at the bottom of the page. + +.. pydantic:: parakeet.config.Config + +The default configuration parameters can be seen by typing the following +command: + +Examples +-------- + +Basic configuration +^^^^^^^^^^^^^^^^^^^ + +This is the default configuration file as output by parakeet.config.new. This configuration file only shows the most useful parameters which you should set. + +.. code-block:: yaml + + microscope: + beam: + electrons_per_angstrom: 30 + energy: 300 + source_spread: 0.1 + detector: + nx: 1000 + ny: 1000 + pixel_size: 1 + lens: + c_10: -20000 + c_30: 2.7 + c_c: 2.7 + sample: + box: + - 1000 + - 1000 + - 1000 + centre: + - 500 + - 500 + - 500 + molecules: null + shape: + cube: + length: 1000.0 + cuboid: + length_x: 1000.0 + length_y: 1000.0 + length_z: 1000.0 + cylinder: + length: 1000.0 + radius: 500.0 + margin: + - 0 + - 0 + - 0 + type: cube + scan: + mode: still + num_images: 1 + start_angle: 0 + step_angle: 0 + simulation: + ice: false + +Full configuration +^^^^^^^^^^^^^^^^^^ + +The full configuration is somewhat longer and contains parameters which may not +be necessary to modify in most cases: + +.. code-block:: yaml + + cluster: + max_workers: 1 + method: null + device: gpu + microscope: + beam: + acceleration_voltage_spread: 8.0e-07 + defocus_drift: null + drift: null + electrons_per_angstrom: 30 + energy: 300 + energy_spread: 2.66e-06 + phi: 0 + source_spread: 0.1 + theta: 0 + detector: + dqe: false + nx: 1000 + ny: 1000 + origin: + - 0 + - 0 + pixel_size: 1 + lens: + c_10: -20000 + c_30: 2.7 + c_c: 2.7 + current_spread: 3.3e-07 + model: null + phase_plate: false + sample: + box: + - 1000 + - 1000 + - 1000 + centre: + - 500 + - 500 + - 500 + ice: null + molecules: null + shape: + cube: + length: 1000.0 + cuboid: + length_x: 1000.0 + length_y: 1000.0 + length_z: 1000.0 + cylinder: + length: 1000.0 + radius: 500.0 + margin: + - 0 + - 0 + - 0 + type: cube + sputter: null + scan: + axis: + - 0 + - 1 + - 0 + exposure_time: 1 + mode: still + num_images: 1 + start_angle: 0 + start_pos: 0 + step_angle: 0 + step_pos: 0 + simulation: + division_thickness: 100 + ice: false + inelastic_model: null + margin: 100 + mp_loss_position: peak + mp_loss_width: null + padding: 100 + radiation_damage_model: false + sensitivity_coefficient: 0.022 + slice_thickness: 3.0 + +Specifying molecule positions +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The following snippet will load one locally defined PDB file and will add a +single instance to the sample model. This will put the molecule in the centre +of the sample volume. + +.. code-block:: yaml + + sample: + molecules: + local: + - filename: myfile.pdb + instances: 1 + +The following snippet will load one locally defined PDB file and will add a 10 +instances to the sample model. This will give the molecules randomly assigned +positions and orientations within the sample volume. + +.. code-block:: yaml + + sample: + molecules: + local: + - filename: myfile.pdb + instances: 10 + +The following snippet will load two locally defined PDB files and one model +from the PDB. The first model had two instances, the first of which has a +random position and random orientation. The second instance has defined +position and random orientation. The second molecule has two instances, the +first of which has random position and defined orientation and the second +instance has defined position and orientation. The PDB model has 10 instances +with random position and orientation. + +.. code-block:: yaml + + sample: + molecules: + local: + - filename: myfile.pdb + instances: + - position: null + orientation: null + - position: [1, 2, 3] + orientation: null + - filename: another.pdb + instances: + - position: null + orientation: [1, 2, 3] + - position: [1, 2, 3] + orientation: [1, 2, 3] + pdb: + - id: 4V5D + instances: 10 + +Applying radiation damage +^^^^^^^^^^^^^^^^^^^^^^^^^ + +Parakeet implements a simple radiation damage model which uses an isotropic B +factor to blur the atomic potential during simulation. The B factor increases +linearly with the incident electron dose according to a sensitivity +coefficient. To apply the beam damage model you can set the following +parameters which will enable the beam damage model and simulate the images +using a dose symmetric scheme. + +.. code-block:: yaml + + simulation: + radiation_damage_model: true + sensitivity_coefficient: 0.022 + + scan: + mode: dose_symmetric diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt new file mode 100644 index 00000000..b2bfa51b --- /dev/null +++ b/docs/_sources/index.rst.txt @@ -0,0 +1,29 @@ +.. parakeet documentation master file, created by + sphinx-quickstart on Fri Feb 25 09:31:39 2022. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to parakeet's documentation! +==================================== + +.. image:: images/parakeet_logo.png + :width: 300 + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + installation + usage + api + configuration + tutorial + publications + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/_sources/installation.rst.txt b/docs/_sources/installation.rst.txt new file mode 100644 index 00000000..369a6958 --- /dev/null +++ b/docs/_sources/installation.rst.txt @@ -0,0 +1,574 @@ +Installation +============ + +Dependencies +------------ + +In order to build this package, the following dependencies are required: + +- A C++ compiler (e.g. g++) +- FFTW +- Python development libraries +- The CUDA toolkit + +On ubuntu 20.04, the dependencies can be install on a clean install as follows +(you may need to contact your system administrator if you do not have admin +privileges): + + +.. code-block:: bash + + # Install GCC + sudo apt-get install build-essential + + # Install FFTW + sudo apt-get install libfftw3-dev + + # Install Python headers + sudo apt-get install python3.8-dev + sudo apt-get install python3.8-venv + + # Install CUDA toolkit + wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin + sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600 + sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub + sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /" + sudo apt-get update + sudo apt-get -y install cuda + +Environment variables +--------------------- + +If you have multiple compiler versions or the compilers you want to use are not +automatically picked up by cmake, you can explicitly state the compiler +versions you would like to use as follows, where in this case we are using gcc +as the C++ compiler: + +.. code-block:: bash + + export CXX=/usr/bin/g++ + export CUDACXX=/usr/local/cuda-11/bin/nvcc + export FFTWDIR=/usr/local/ + +Depending on your GPU and the version of the CUDA toolkit you are using, it may +also be necessary to set the CMAKE_CUDA_ARCHITECTURES variable. This variable +is by default set to "OFF" in the CMakeLists.txt file which has the effect of +compiling CUDA kernels on the fly. If you have an old GPU, this may not work +and you will receive CUDA errors when attempting to run the simulations on the +GPU. In this case simply set the variable to the architecture supported by your +GPU as follows (the example below is for the compute_37 architecture): + +.. code-block:: bash + + export CMAKE_CUDA_ARCHITECTURES=37 + + +Python virtual environments +--------------------------- + +Before installing parakeet, you may want to setup a python virtual environment +in which to install it rather than installing into your system library. Use the +following commands before following the instructions below. + +.. code-block:: bash + + python3 -m venv env + source env/bin/activate + + +Install from source +------------------- + +To install from source you can run the following commands after setting the +environment variables described above. + +.. code-block:: bash + + # Clone the repository + git clone https://github.com/rosalindfranklininstitute/parakeet.git + + # Enter the parakeet directory + cd parakeet + + # Checkout the submodules + git submodule update --init --recursive + + # Install the package locally + pip install . + + +.. _Installation for developers: + +Installation for developers +--------------------------- + +Run the following commands to install in development mode after setting the +environment variables described above: + +.. code-block:: bash + + # Clone the repository + git clone https://github.com/rosalindfranklininstitute/parakeet.git + + # Enter the parakeet directory + cd parakeet + + # Checkout the submodules + git submodule update --init --recursive + + # Install the package locally + pip install . -e + + +Install using PIP +----------------- + +You can install parakeet from the python package archive using pip by running +the following command. This is a source package which needs to be built on your +local machine so the environment variables described above for CUDA, FFTW and +CXX may need to be set. + +.. code-block:: bash + + pip install python-parakeet + +It is also possible to install the version of parakeet on the master branch (or +any other branch) directly using pip by using the following command: + +.. code-block:: bash + + python -m pip install git+https://github.com/rosalindfranklininstitute/parakeet.git@master + +Install using conda +------------------- + +You can install parakeet using conda as follows: + +.. code-block:: bash + + # Create a conda environment + conda create -n parakeet python=3.9 + + # Install parakeet + conda install -c conda-forge -c james.parkhurst python-parakeet + + +Install as a Docker container +----------------------------- + +Parakeet can also be run via Docker +(https://www.docker.com/get-started). To pull the docker container with the latest version +parakeet, you can do the following: + +.. code-block:: bash + + docker pull quay.io/rosalindfranklininstitute/parakeet:latest + +You may also pull the docker container of a specific version of parakeet. To do this in the above +command replace the 'latest' with one of the tags that you can find here +( https://quay.io/repository/rosalindfranklininstitute/parakeet?tab=tags). + +To use parakeet with docker with GPU support the host machine should have the +appropriate Nvidia drivers installed and docker needs to be installed with the +nvidia container toolkit +(https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html). + +To easily input and output data from the container the volume mechanism can be +used, where a workspace directory of the host machine is mounted to a directory +in the container (in the folder /mnt in the example below). For this reason it +is advised that all the relevant files (e.g. config.yaml, sample.h5, etc.) +should be present in the host workspace directory. + +Below is an example on how to use parakeet after, its docker image has been pulled, to run parakeet commands: + +.. code-block:: bash + + docker run --gpus all -v $(pwd):/mnt --workdir=/mnt parakeet:latest \ + parakeet.config.new + +You may also pull and run parakeet with a single command. + +.. code-block:: bash + + docker run --gpus all -v $(pwd):/mnt --workdir=/mnt \ + quay.io/rosalindfranklininstitute/parakeet:latest parakeet.config.new + + +Install as a Singularity image +------------------------------ + +Parakeet can also be run via Singularity +(https://sylabs.io/guides/2.6/user-guide/installation.html). To build +parakeet's singularity container you can do the following: + +.. code-block:: bash + + singularity build parakeet.sif docker://quay.io/rosalindfranklininstitute/parakeet:latest + +Again similar to docker, you may build the singularity container of a specific version of parakeet +by replacing the 'latest' in the command above with one of the tags that you can find here +( https://quay.io/repository/rosalindfranklininstitute/parakeet?tab=tags). + +Also like with docker, to use parakeet with singularity and GPU support, the +host machine should have the appropriate Nvidia drivers installed. + +Below is an example on how to use parakeet, after its singularity image has been build, to run parakeet commands: + +.. code-block:: bash + + # You can open an interactive shell in the singularity container like this: + singularity shell --nv --bind=/data/directory:/mnt --pwd=/mnt parakeet.sif + + # Or you can execute multiple commands + singularity exec --nv --bind=/data/directory:/mnt --pwd=/mnt parakeet.sif \ + bash -c "parakeet.config.new && parakeet.sample.new" + +You may also build and run parakeet with a single command. + +.. code-block:: bash + + # You can open an interactive shell in the singularity container like this: + singularity shell --nv --bind=/data/directory:/mnt --pwd=/mnt \ + docker://quay.io/rosalindfranklininstitute/parakeet:latest + + # Or you can execute multiple commands + singularity exec --nv --bind=/data/directory:/mnt --pwd=/mnt \ + docker://quay.io/rosalindfranklininstitute/parakeet:latest \ + bash -c "parakeet.config.new && parakeet.sample.new" + + +Install as Singularity sandbox +------------------------------ + +If you need to modify the singularity container for development purposes, it is +possible to build a parakeet sandbox as follows: + +.. code-block:: bash + + singularity build --sandbox parakeet_sandbox/ parakeet.sif + +The source code for parakeet resides in the parakeet_sandbox/apps/ directory. +You can then modify the python code in place and use `singularity shell` or +`singularity run` to install the changes as follows: + +.. code-block:: bash + + singularity run --writable parakeet_sandbox/ pip install /app --prefix=/usr/local + +Likewise, new software packages can be install into the container as follows: + +.. code-block:: bash + + singularity run --writable parakeet_sandbox/ pip install ${PACKAGE} --prefix=/usr/local + +To run parakeet from the sandbox, execute with the following command: + +.. code-block:: bash + + singularity run --nv parakeet_sandbox/ parakeet.run -c config.yaml + + +If you want to rebuild the singularity image from the sandbox you can then do +the following: + +.. code-block:: bash + + singularity build parakeet_image.sif parakeet_sandbox/ + + +Build a derivative Singularity image +------------------------------------ + +You can build a new container depending on the parakeet docker container as +follows. In your python source code repository create a file called Dockerfile +with the following contents: + +.. code-block:: bash + + FROM quay.io/rosalindfranklininstitute/parakeet:latest + + WORKDIR /myapp + COPY . . + + RUN apt update + RUN git submodule update --init --recursive + RUN pip install . + +Now build locally with docker: + +.. code-block:: bash + + sudo docker build . -t me/myapp + +Now we can build the singularity image from the docker image + +.. code-block:: bash + + singularity build myapp.sif docker-daemon://me/myapp:latest + + +Install as a Apptainer image +------------------------------ + +Parakeet can also be run via Apptainer. Apptainer is the new name for the Singularity +project after is official move to the Linux Foundation +(https://apptainer.org/news/community-announcement-20211130/). + +You may build and run parakeet via an Apptainer container the same way you would +build and run parakeet via an Singularity container, but instead of the command +'singularity' the command 'apptainer' should be used. The arguments of the command +'apptainer' is the exact same with the command 'singularity'. + + +Install as a snap +----------------- + +You can install the parakeet snap from the snapcraft repository as follows: + +.. code-block:: bash + + # Install the snap from the edge channel + sudo snap install parakeet --classic --edge + +You can also build the parakeet snap application from source as follows: + +.. code-block:: bash + + # Run this command in the repository directory on a VM with 4GB memory + SNAPCRAFT_BUILD_ENVIRONMENT_MEMORY=4G snapcraft + + # Install the locally built snap + sudo snap install parakeet_${VERSION}.snap --classic --dangerous + +Note that the snap installation only exposes the top level parakeet command: + +.. code-block:: bash + + parakeet -h + + +Install on Baskerville HPC (native) +----------------------------------- + +In order to install parakeet on the Baskerville tier 2 supercomputer (https://www.baskerville.ac.uk/) +within a virtual python environment (https://docs.baskerville.ac.uk/self-install/), +start an interactive job as follows (you will need to know your +account-project code and qos to do this): + +.. code-block:: bash + + srun --account=${ACCOUNT} --qos=${QOS} --gpus=1 --time=0:20:0 \ + --export=USER,HOME,PATH,TERM --pty /bin/bash + +When the interactive job starts (you may need to wait until the requested computational resources are +available), execute the following commands to install parakeet: + +.. code-block:: bash + + # Load required modules + module purge + module load baskerville + module load CUDA/11.4 + module load FFTW + module load Python/3 + + # Create a virtual environment + python -m venv --system-site-packages env + source env/bin/activate + python -m pip install pip --upgrade + + # Install parakeet + python -m pip install python-parakeet + +You can run parakeet on Baskerville non-interactively and interactively. + +To run parakeet on Baskerville non-interactively (https://docs.baskerville.ac.uk/jobs/) +you need write a script called run.sh with the following contents (you will need to know +your account-project code, qos and how much time do you expect to take for your script to finish): + +.. code-block:: bash + + #!/bin/bash + #SBATCH --account=$ACCOUNT + #SBATCH --qos=$QOS + #SBATCH --gpus=1 + #SBATCH --time=$TIME + + # Load required modules + module purge + module load baskerville + module load CUDA/11.4 + module load FFTW + module load Python/3 + + # Activate environment + source env/bin/activate + + # Parakeet commands + parakeet.run -c config.yaml + +To submit the run.sh script and therefore run the parakeet simulations execute the following: + +.. code-block:: bash + + sbatch run.sh + +The benefit of non-interactive job submissions is that your job will be executed automatically, +when the requested computational resources are available and that you can submit and queue multiple +jobs. + +To run parakeet interactively (https://docs.baskerville.ac.uk/interactive-jobs/), execute: + +.. code-block:: bash + + srun --account=${ACCOUNT} --qos=${QOS} --gpus=1 --time=${TIME} \ + --export=USER,HOME,PATH,TERM --pty /bin/bash + +When the interactive job starts (you may need to wait until the requested computational resources are +available), execute the following commands to install parakeet: + +.. code-block:: bash + + # Load required modules + module purge + module load baskerville + module load CUDA/11.4 + module load FFTW + module load Python/3 + + # Activate environment + source env/bin/activate + + # Parakeet commands + parakeet.run -c config.yaml + +Install on Baskerville (apptainer) +------------------------------------ + +Alternatively, you may run parakeet on the baskerville tier 2 supercomputer with +apptainer (https://docs.baskerville.ac.uk/containerisation/). + +To run parakeet on Baskerville non-interactively (https://docs.baskerville.ac.uk/jobs/) +you need write a script called run.sh with the following contents (you will need to know +your account-project code, qos and how much time do you expect to take for your script to finish): + +.. code-block:: bash + + #!/bin/bash + #SBATCH --account=$ACCOUNT + #SBATCH --qos=$QOS + #SBATCH --gpus=1 + #SBATCH --time=$TIME + + # Load required modules + module purge + module load baskerville + module load CUDA/11.4 + module load FFTW + module load Python/3 + + export APPTAINER_CACHEDIR=/path/to/cache/directory/within/your/project/directory + + function container { + apptainer exec --nv --bind=/path/to/data/directory/within/your/project/directory:/mnt --pwd=/mnt \ + docker://quay.io/rosalindfranklininstitute/parakeet:latest bash -c "$@" + } + + # Parakeet commands + container \ + "echo Below you can have multiple commands && \ + parakeet.run -c config.yaml" + +To submit the run.sh script and therefore run the parakeet simulations execute the following: + +.. code-block:: bash + + sbatch run.sh + +The benefit of non-interactive job submissions is that your job will be executed automatically, +when the requested computational resources are available and that you can submit and queue multiple +jobs. + +To run parakeet interactively (https://docs.baskerville.ac.uk/interactive-jobs/), execute: + +.. code-block:: bash + + srun --account=${ACCOUNT} --qos=${QOS} --gpus=1 --time=${TIME} \ + --export=USER,HOME,PATH,TERM --pty /bin/bash + +When the interactive job starts (you may need to wait until the requested computational resources are +available), execute the following commands to install parakeet: + +.. code-block:: bash + + # Load required modules + module purge + module load baskerville + module load CUDA/11.4 + module load FFTW + module load Python/3 + + export APPTAINER_CACHEDIR=/path/to/cache/directory/within/your/project/directory + + function container { + apptainer exec --nv --bind=/path/to/data/directory/within/your/project/directory:/mnt --pwd=/mnt \ + docker://quay.io/rosalindfranklininstitute/parakeet:latest bash -c "$@" + } + + # Parakeet commands + container \ + "echo Below you can have multiple commands && \ + parakeet.run -c config.yaml" + + +Install on STFC Scarf +--------------------- + +In order to install parakeet on the scarf with singularity, start and +interactive job as follows: + +.. code-block:: bash + + salloc --time=1:0:0 + +Now run the following commands: + +.. code-block:: bash + + singularity build parakeet.sif docker://quay.io/rosalindfranklininstitute/parakeet:latest + +Once you are happy, log out of the interactive node. To run parakeet on scarf +write a script called run.sh with the following contents: + +.. code-block:: bash + + #!/bin/bash + #SBATCH --gpus=1 + + function container { + singularity exec --nv --bind=/path/to/data/directory/within/your/project/directory:/mnt --pwd=/mnt \ + docker://quay.io/rosalindfranklininstitute/parakeet:latest bash -c "$@" + } + + # Parakeet commands + container \ + "echo Below you can have multiple commands && \ + parakeet.run -c config.yaml" + +Then run the simulations as follows: + +.. code-block:: bash + + sbatch run.sh + + +Testing +------- + +To run the tests, follow the :ref:`Installation for developers` instructions +and then do the following command from within the source distribution: + +.. code-block:: bash + + pytest + diff --git a/docs/_sources/publications.rst.txt b/docs/_sources/publications.rst.txt new file mode 100644 index 00000000..45adb87d --- /dev/null +++ b/docs/_sources/publications.rst.txt @@ -0,0 +1,10 @@ +Publications +============ + +If you find parakeet useful for you work, please consider citing our paper: + + Parkhurst, J. M., Dumoux, M., Basham, M., Clare, D., Siebert, C. A., Varslot, + T., Kirkland, A., Naismith, J. H., & Evans, G. (2021). Parakeet: A digital + twin software pipeline to assess the impact of experimental parameters on + tomographic reconstructions for cryo-electron tomography. Open Biology, + 11(10). https://doi.org/10.1098/rsob.210160 diff --git a/docs/_sources/tutorial.rst.txt b/docs/_sources/tutorial.rst.txt new file mode 100644 index 00000000..9429e346 --- /dev/null +++ b/docs/_sources/tutorial.rst.txt @@ -0,0 +1,216 @@ +Tutorial +======== + +Simulation of datasets is split into a number of different commands. Each +command takes a set of command line options or a configuration file in YAML +format. + +Generate a new configuration file +--------------------------------- + +.. code-block:: bash + + parakeet.config.new + +This will generate a new file called config.yaml which will contain the +following configuration. + +.. code-block:: yaml + + microscope: + beam: + electrons_per_angstrom: 30 + energy: 300 + source_spread: 0.1 + detector: + nx: 1000 + ny: 1000 + pixel_size: 1 + lens: + c_10: -20000 + c_30: 2.7 + c_c: 2.7 + sample: + box: + - 1000 + - 1000 + - 1000 + centre: + - 500 + - 500 + - 500 + molecules: null + shape: + cube: + length: 1000.0 + cuboid: + length_x: 1000.0 + length_y: 1000.0 + length_z: 1000.0 + cylinder: + length: 1000.0 + radius: 500.0 + margin: + - 0 + - 0 + - 0 + type: cube + scan: + mode: still + num_images: 1 + start_angle: 0 + step_angle: 0 + simulation: + ice: false + +Edit the configuration file +--------------------------- + +The configuration file now needs to be edited to perform the desired +simulation. For example, to simulate with a single molecule we modify the +sample.molecules field as follows. + +.. code-block:: yaml + + microscope: + beam: + electrons_per_angstrom: 30 + energy: 300 + source_spread: 0.1 + detector: + nx: 1000 + ny: 1000 + pixel_size: 1 + lens: + c_10: -20000 + c_30: 2.7 + c_c: 2.7 + sample: + box: + - 1000 + - 1000 + - 1000 + centre: + - 500 + - 500 + - 500 + molecules: + pdb: + - id: 4v1w + instances: 1 + shape: + cube: + length: 1000.0 + cuboid: + length_x: 1000.0 + length_y: 1000.0 + length_z: 1000.0 + cylinder: + length: 1000.0 + radius: 500.0 + margin: + - 0 + - 0 + - 0 + type: cube + scan: + mode: still + num_images: 1 + start_angle: 0 + step_angle: 0 + simulation: + ice: false + +Generate sample model +--------------------- + +Once the configuration file has been generated a new sample file can be created +with the following command: + +.. code-block:: bash + + parakeet.sample.new -c config.yaml + + +This will result in a file "sample.h5" being generated. This file contains +information about the size and shape of the sample but as yet doesn't contain +any atomic coordinates. The atomic model is added by running the following +command which adds molecules to the sample file. If a single molcule is +specified then it will be placed in the centre of the sample volume. If +multiple molecules are specified then the molecules will be positioned at +random locations in the sample volume. This command will update the "sample.h5" +file with the atomic coordinates but will not generated any new files. + +.. code-block:: bash + + parakeet.sample.add_molecules -c config.yaml + + +Simulate EM images +------------------ + +Once the atomic model is ready, the EM images can be simulated with the +following commands. Each stage of the simulation is separated because it may be +desirable to simulate many different defocused images from the sample exit wave +for example or many different doses for the sample defocusses image. Being +separate, the output of one stage can be reused for multiple runs of the next +stage. The first stage is to simulate the exit wave. This is the propagation of +the electron wave through the sample. It is therefore the most computationally +intensive part of the processes since the contribution of all atoms within the +sample needs to be calculated. + + +.. code-block:: bash + + parakeet.simulate.exit_wave -c config.yaml + + +This command will generate a file "exit_wave.h5" which will contain the exit +wave of all tilt angles. The next step is to simulate the micropscope optics +which is done with the following command: + +.. code-block:: bash + + parakeet.simulate.optics -c config.yaml + + +This step is much quicker as it only scales with the size of the detector image +and doesn't require the atomic coordinates again. The command will output a +file "optics.h5". Finally, the response of the detector can be simulated with +the following command: + +.. code-block:: bash + + parakeet.simulate.image -c config.yaml + + +This command will add the detector DQE and the Poisson noise for a given dose +and will output a file "image.h5". + +Export functions +---------------- + +Typically we cant to output an MRC file for further processing. The hdf5 files +can easily be exported to MRC by the following command: + +.. code-block:: bash + + parakeet.export file.h5 -o file.mrc + +The export command can also be used to rebin the image or select a region of interest. + +Analysis functions +------------------ + +The reconstruction function can be called in Parakeet in the following way: + +.. code-block:: bash + + parakeet.export image.h5 -o image.mrc + parakeet.analyse.reconstruct -c config.yaml -i image.mrc + +Averaging of the particles can then be done with: + +.. code-block:: bash + + parakeet.analyse.average_particles -c config.yaml diff --git a/docs/_sources/usage.rst.txt b/docs/_sources/usage.rst.txt new file mode 100644 index 00000000..e3b6d21d --- /dev/null +++ b/docs/_sources/usage.rst.txt @@ -0,0 +1,225 @@ +Command line programs +===================== + +Config file manipulation programs +--------------------------------- + +parakeet.config.new +^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.config._new + :func: get_parser + :prog: parakeet.config.new + +parakeet.config.show +^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.config._show + :func: get_parser + :prog: parakeet.config.show + +parakeet.config.edit +^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.config._edit + :func: get_parser + :prog: parakeet.config.edit + +Sample manipulation programs +---------------------------- + +parakeet.sample.new +^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.sample._new + :func: get_parser + :prog: parakeet.sample.new + +parakeet.sample.add_molecules +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.sample._add_molecules + :func: get_parser + :prog: parakeet.sample.add_molecules + +parakeet.sample.mill +^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.sample._mill + :func: get_parser + :prog: parakeet.sample.mill + +parakeet.sample.sputter +^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.sample._sputter + :func: get_parser + :prog: parakeet.sample.sputter + +parakeet.sample.show +^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.sample._show + :func: get_parser + :prog: parakeet.sample.show + + +Image Simulation programs +------------------------- + +parakeet.simulate.potential +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.simulate._potential + :func: get_parser + :prog: parakeet.simulate.potential + +parakeet.simulate.exit_wave +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.simulate._exit_wave + :func: get_parser + :prog: parakeet.simulate.exit_wave + +parakeet.simulate.optics +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.simulate._optics + :func: get_parser + :prog: parakeet.simulate.optics + +parakeet.simulate.ctf +^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.simulate._ctf + :func: get_parser + :prog: parakeet.simulate.ctf + +parakeet.simulate.image +^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.simulate._image + :func: get_parser + :prog: parakeet.simulate.image + +parakeet.simulate.simple +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.simulate._simple + :func: get_parser + :prog: parakeet.simulate.simple + + +Analysis programs +----------------- + +parakeet.analyse.reconstruct +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.analyse._reconstruct + :func: get_parser + :prog: parakeet.analyse.reconstruct + +parakeet.analyse.correct +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.analyse._correct + :func: get_parser + :prog: parakeet.analyse.correct + +parakeet.analyse.average_particles +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.analyse._average_particles + :func: get_parser + :prog: parakeet.analyse.average_particles + +parakeet.analyse.average_all_particles +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.analyse._average_all_particles + :func: get_parser + :prog: parakeet.analyse.average_all_particles + +parakeet.analyse.extract +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.analyse._extract + :func: get_parser + :prog: parakeet.analyse.extract + + +parakeet.analyse.refine +^^^^^^^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.analyse._refine + :func: get_parser + :prog: parakeet.analyse.refine + + +PDB file programs +------------------ + +parakeet.pdb.read +^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.pdb._read + :func: get_parser + :prog: parakeet.pdb.read + +parakeet.pdb.get +^^^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line.pdb._get + :func: get_parser + :prog: parakeet.pdb.get + + +Other programs +-------------- + +parakeet.export +^^^^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line._export + :func: get_parser + :prog: parakeet.export + +parakeet.run +^^^^^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line._run + :func: get_parser + :prog: parakeet.run + +parakeet +^^^^^^^^ + +.. argparse:: + :module: parakeet.command_line._main + :func: get_parser + :prog: parakeet diff --git a/docs/_static/_sphinx_javascript_frameworks_compat.js b/docs/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/docs/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See 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Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + 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font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #BA2121 } /* Literal.String.Double */ +.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js new file mode 100644 index 00000000..b08d58c9 --- /dev/null +++ b/docs/_static/searchtools.js @@ -0,0 +1,620 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/docs/_static/sphinx_highlight.js b/docs/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/docs/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/docs/api.html b/docs/api.html new file mode 100644 index 00000000..ccbf4a68 --- /dev/null +++ b/docs/api.html @@ -0,0 +1,1259 @@ + + + + + + + + + Python API — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Python API

+
+

Warning

+

This is under developement

+
+

The functionality of the command line programs can be called from python as shown below.

+
+

Image IO functions

+
+
+parakeet.io.new(filename, shape=None, pixel_size=1, dtype='float32', vmin=None, vmax=None)
+

Create a new file for writing

+
+
Parameters:
+
    +

  • filename (str) – The output filename

    • +

  • shape (tuple) – The output shape

    • +

  • pixel_size (tuple) – The pixel size

    • +

  • dtype (object) – The data type (only used with NexusWriter)

    • +

  • vmin (int) – The minimum value (only used in ImageWriter)

    • +

  • vmax (int) – The maximum value (only used in ImageWriter)

    • +
+
+
Returns:
+

The file writer

+
+
Return type:
+

object

+
+
+
+ +
+
+parakeet.io.open(filename)
+

Read the simulated data from file

+
+
Parameters:
+

filename (str) – The output filename

+
+
+
+ +
+
+

PDB file functions

+
+
+parakeet.data.get_pdb(name)
+

Return the path to the data file

+
+
Parameters:
+

name (str) – The pdb id

+
+
Returns:
+

The absolute filename

+
+
Return type:
+

str

+
+
+
+ +
+
+

Configuration functions

+
+
+parakeet.config.new(filename: str = 'config.yaml', full: bool = False) → Config
+

Generate a new config file

+
+
Parameters:
+
    +

  • filename – The config filename

    • +

  • full – Full or basic configuration

    • +
+
+
+
+ +
+
+

Sample functions

+
+
+parakeet.sample.new(config_file, sample_file: str) → Sample
+
+parakeet.sample.new(config: Config, filename: str) → Sample
+
+parakeet.sample.new(config: Sample, filename: str) → Sample
+

Create an ice sample and save it

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The sample filename

    • +
+
+
+
+ +
+
+parakeet.sample.add_molecules(config_file, sample_file: str) → Sample
+
+parakeet.sample.add_molecules(config: Config, sample_file: str) → Sample
+
+parakeet.sample.add_molecules(config: Sample, sample: Sample) → Sample
+

Add molecules to the sample

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The input sample filename

    • +
+
+
+
+ +
+
+parakeet.sample.mill(config_file, sample_file: str) → Sample
+
+parakeet.sample.mill(config: Config, sample_file: str) → Sample
+
+parakeet.sample.mill(config: Sample, sample: Sample) → Sample
+

Mill to the shape of the sample

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The sample filename

    • +
+
+
Returns:
+

The sample object

+
+
+
+ +
+
+parakeet.sample.sputter(config_file, sample_file: str) → Sample
+
+parakeet.sample.sputter(config: Config, sample_file: str) → Sample
+
+parakeet.sample.sputter(config: Sputter, sample: Sample) → Sample
+

Sputter the sample

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The sample filename

    • +
+
+
+
+ +
+
+

Image simulation functions

+
+
+parakeet.simulate.potential(config_file, sample_file: str, potential_prefix: str, device: Device = None, nproc: int = None, gpu_id: list = None)
+
+parakeet.simulate.potential(config: Config, sample_file: str, potential_prefix: str)
+

Simulate the projected potential from the sample

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The input sample filename

    • +

  • potential_prefix – The input potential filename

    • +

  • device – The device to run on (cpu or gpu)

    • +

  • nproc – The number of processes

    • +

  • gpu_id – The list of gpu ids

    • +
+
+
+
+ +
+
+parakeet.simulate.exit_wave(config_file, sample_file: str, exit_wave_file: str, device: Device = None, nproc: int = None, gpu_id: list = None)
+
+parakeet.simulate.exit_wave(config: Config, sample: Sample, exit_wave_file: str)
+

Simulate the exit wave from the sample

+
+
Parameters:
+
    +

  • config_file – The config filename

    • +

  • sample_file – The sample filename

    • +

  • exit_wave_file – The exit wave filename

    • +

  • device – The device to run on (cpu or gpu)

    • +

  • nproc – The number of processes

    • +

  • gpu_id – The list of gpu ids

    • +
+
+
+
+ +
+
+parakeet.simulate.optics(config_file, exit_wave_file: str, optics_file: str, device: Device = None, nproc: int = None, gpu_id: list = None)
+
+parakeet.simulate.optics(config: Config, exit_wave_file: str, optics_file: str)
+

Simulate the optics

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • exit_wave_file – The input exit wave filename

    • +

  • optics_file – The output optics filename

    • +

  • device – The device to run on (cpu or gpu)

    • +

  • nproc – The number of processes

    • +

  • gpu_id – The list of gpu ids

    • +
+
+
+
+ +
+
+parakeet.simulate.image(config_file, optics_file: str, image_file: str)
+
+parakeet.simulate.image(config: Config, optics_file: str, image_file: str)
+

Simulate the image with noise

+
+
Parameters:
+
    +

  • config_file – The config filename

    • +

  • optics_file – The optics image filename

    • +

  • image_file – The output image filename

    • +
+
+
+
+ +
+
+parakeet.simulate.ctf(config_file, output_file: str)
+
+parakeet.simulate.ctf(config: Config, output_file: str)
+

Simulate the ctf

+
+
Parameters:
+
    +

  • config_file – The config filename

    • +

  • output_file – The output ctf filename

    • +
+
+
+
+ +
+
+

Analysis functions

+
+
+parakeet.analyse.correct(config_file, image_file: str, corrected_file: str, num_defocus: int = 1, device: Device = None)
+
+parakeet.analyse.correct(config: Config, image_filename: str, corrected_filename: str, num_defocus: int | None = None)
+

Correct the images using 3D CTF correction

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • image_file – The input image filename

    • +

  • corrected_file – The output CTF corrected filename

    • +

  • num_defocus – The number of defoci

    • +

  • device – The device to use (CPU or GPU)

    • +
+
+
+
+ +
+
+parakeet.analyse.reconstruct(config_file, image_file: str, rec_file: str, device: Device = None)
+
+parakeet.analyse.reconstruct(config: Config, image_filename: str, rec_filename: str)
+

Reconstruct the volume

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • image_file – The input image filename

    • +

  • rec_file – The output CTF corrected reconstruction filename

    • +

  • device – The device to use (CPU or GPU)

    • +
+
+
+
+ +
+
+parakeet.analyse.average_particles(config_file, sample_file: str, rec_file: str, half1_file: str, half2_file: str, particle_size: int, num_particles: int)
+
+parakeet.analyse.average_particles(config: Scan, sample: Sample, rec_filename: str, half_1_filename: str, half_2_filename: str, particle_size: int = 0, num_particles: int = 0)
+

Perform sub tomogram averaging

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The sample filename

    • +

  • rec_file – The reconstruction filename

    • +

  • half1_file – The particle average filename for half 1

    • +

  • half2_file – The particle average filename for half 2

    • +

  • particle_size – The particle size (px)

    • +

  • num_particles – The number of particles to average

    • +
+
+
+
+ +
+
+parakeet.analyse.average_all_particles(config_file, sample_file: str, rec_file: str, average_file: str, particle_size: int, num_particles: int)
+
+parakeet.analyse.average_all_particles(config: Scan, sample: Sample, rec_filename: str, average_filename: str, particle_size: int = 0, num_particles: int = 0)
+

Perform sub tomogram averaging

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The sample filename

    • +

  • rec_file – The reconstruction filename

    • +

  • average_file – The particle average filename

    • +

  • particle_size – The particle size (px)

    • +
+
+
+
+ +
+
+parakeet.analyse.extract(config_file, sample_file: str, rec_file: str, particles_file: str, particle_size: int, particle_sampling: int)
+
+parakeet.analyse.extract(config: Config, sample: Sample, rec_filename: str, extract_file: str, particle_size: int = 0, particle_sampling: int = 1)
+

Perform sub tomogram extraction

+
+
Parameters:
+
    +

  • config_file – The input config filename

    • +

  • sample_file – The sample filename

    • +

  • rec_file – The reconstruction filename

    • +

  • particles_file – The file to extract the particles to

    • +

  • particle_size – The particle size (px)

    • +

  • particle_sampling – The particle sampling (factor of 2)

    • +
+
+
+
+ +
+
+parakeet.analyse.refine(sample_filename: str, rec_filename: str)
+

Refine the molecule against the map

+
+ +
+
+parakeet.run(config_file, sample_file: str, exit_wave_file: str, optics_file: str, image_file: str, device: Device = None, nproc: int = None, gpu_id: list = None, steps: list = None)
+
+parakeet.run(config: Config, sample_file: str, exit_wave_file: str, optics_file: str, image_file: str, steps: list | None = None)
+

Simulate the TEM image from the sample

+

If steps is None then all steps are run, otherwise steps is +a list which contains one or more of the following: all, sample, simulate, +sample.new, sample.add_molecules, simulate.exit_wave, simulate.optics and +simulate.image

+
+
Parameters:
+
    +

  • config_file – The config filename

    • +

  • sample_file – The sample filename

    • +

  • exit_wave_file – The exit wave filename

    • +

  • optics_file – The optics filename

    • +

  • image_file – The image filename

    • +

  • device – The device to run on (cpu or gpu)

    • +

  • nproc – The number of processes

    • +

  • gpu_id – The list of gpu ids

    • +

  • steps – Choose the steps to run

    • +
+
+
+
+ +
+
+

Data models

+
+
+class parakeet.beam.Beam(energy: float = 300, energy_spread: float = 0, acceleration_voltage_spread: float = 0, illumination_semiangle: float = 0.1, electrons_per_angstrom: float = 40, theta: float = 0, phi: float = 0, incident_wave: str | None = None)
+

A class to encapsulate a beam

+
+
+__init__(energy: float = 300, energy_spread: float = 0, acceleration_voltage_spread: float = 0, illumination_semiangle: float = 0.1, electrons_per_angstrom: float = 40, theta: float = 0, phi: float = 0, incident_wave: str | None = None)
+

Initialise the beam

+
+
Parameters:
+
    +

  • energy – The beam energy (keV)

    • +

  • energy_spread – dE / E where dE is the 1/e half width

    • +

  • acceleration_voltage_spread – dV / V where dV is the 1 / e half width

    • +

  • illumination_semiangle – The illumination semiangle spread (mrad)

    • +

  • electrons_per_angstrom – The number of electrons per angstrom

    • +

  • theta – The beam tilt theta

    • +

  • phi – The beam tilt phi

    • +

  • incident_wave – The wave function

    • +
+
+
+
+ +
+
+property acceleration_voltage_spread: float
+

dV / V where dV is the 1 / e half width

+
+ +
+
+property electrons_per_angstrom: float
+

The number of electrons per angstrom

+
+ +
+
+property energy: float
+

The beam energy (keV)

+
+ +
+
+property energy_spread: float
+

dE / E where dE is the 1/e half width

+
+ +
+
+property illumination_semiangle: float
+

The illumination semiangle (mrad)

+
+ +
+
+property phi: float
+

The beam tilt phi

+
+ +
+
+property theta: float
+

The beam tilt theta

+
+ +
+ +
+
+class parakeet.detector.Detector(nx: int = 0, ny: int = 0, pixel_size: float = 1, origin: Tuple[float, float, float] = (0, 0, 0), dqe: bool = True)
+

A class to encapsulate a detector

+
+
+__init__(nx: int = 0, ny: int = 0, pixel_size: float = 1, origin: Tuple[float, float, float] = (0, 0, 0), dqe: bool = True)
+

Initialise the detector

+
+
Parameters:
+
    +

  • nx – The size of the detector in X

    • +

  • ny – The size of the detector in Y

    • +

  • pixel_size – The effective size of the pixels in A

    • +

  • origin – The detector origin (A, A)

    • +

  • dqe – Use the detector DQE

    • +
+
+
+
+ +
+ +
+
+class parakeet.lens.Lens(m: int = 0, c_10: float = 20, c_12: float = 0.0, phi_12: float = 0.0, c_21: float = 0.0, phi_21: float = 0.0, c_23: float = 0.0, phi_23: float = 0.0, c_30: float = 0.04, c_32: float = 0.0, phi_32: float = 0.0, c_34: float = 0.0, phi_34: float = 0.0, c_41: float = 0.0, phi_41: float = 0.0, c_43: float = 0.0, phi_43: float = 0.0, c_45: float = 0.0, phi_45: float = 0.0, c_50: float = 0.0, c_52: float = 0.0, phi_52: float = 0.0, c_54: float = 0.0, phi_54: float = 0.0, c_56: float = 0.0, phi_56: float = 0.0, inner_aper_ang: float = 0.0, outer_aper_ang: float = 0.0, c_c: float = 0.0, current_spread: float = 0.0)
+

A class to encapsulate a lens

+
+
+__init__(m: int = 0, c_10: float = 20, c_12: float = 0.0, phi_12: float = 0.0, c_21: float = 0.0, phi_21: float = 0.0, c_23: float = 0.0, phi_23: float = 0.0, c_30: float = 0.04, c_32: float = 0.0, phi_32: float = 0.0, c_34: float = 0.0, phi_34: float = 0.0, c_41: float = 0.0, phi_41: float = 0.0, c_43: float = 0.0, phi_43: float = 0.0, c_45: float = 0.0, phi_45: float = 0.0, c_50: float = 0.0, c_52: float = 0.0, phi_52: float = 0.0, c_54: float = 0.0, phi_54: float = 0.0, c_56: float = 0.0, phi_56: float = 0.0, inner_aper_ang: float = 0.0, outer_aper_ang: float = 0.0, c_c: float = 0.0, current_spread: float = 0.0)
+

Initialise the lens

+
+
Parameters:
+
    +

  • m – The vortex momentum

    • +

  • c_10 – The defocus (A)

    • +

  • c_12 – The 2-fold astigmatism (A)

    • +

  • phi_12 – The azimuthal angle of 2-fold astigmatism (degrees)

    • +

  • c_21 – The axial coma (A)

    • +

  • phi_21 – The azimuthal angle of axial coma (degrees)

    • +

  • c_23 – The 3-fold astigmatism (A)

    • +

  • phi_23 – The azimuthal angle of 3-fold astigmatism (degrees)

    • +

  • c_30 – The 3rd order spherical aberration (mm)

    • +

  • c_32 – The axial star aberration (A)

    • +

  • phi_32 – The azimuthal angle of axial star aberration (degrees)

    • +

  • c_34 – The 4-fold astigmatism (A)

    • +

  • phi_34 – The azimuthal angle of 4-fold astigmatism (degrees)

    • +

  • c_41 – The 4th order axial coma (A)

    • +

  • phi_41 – The azimuthal angle of 4th order axial coma (degrees)

    • +

  • c_43 – The 3-lobe aberration (A)

    • +

  • phi_43 – The azimuthal angle of 3-lobe aberration (degrees)

    • +

  • c_45 – The 5-fold astigmatism (A)

    • +

  • phi_45 – The azimuthal angle of 5-fold astigmatism (degrees)

    • +

  • c_50 – The 5th order spherical aberration (mm)

    • +

  • c_52 – The 5th order axial star aberration (A)

    • +

  • phi_52 – The azimuthal angle of 5th order axial star aberration (degrees)

    • +

  • c_54 – The 5th order rosette aberration (A)

    • +

  • phi_54 – The azimuthal angle of 5th order rosette aberration (degrees)

    • +

  • c_56 – The 6-fold astigmatism (A)

    • +

  • phi_56 – The azimuthal angle of 6-fold astigmatism (degrees)

    • +

  • inner_aper_ang – The inner aperture (mrad)

    • +

  • outer_aper_ang – The outer aperture (mrad)

    • +

  • c_c – The chromatic abberation (mm)

    • +

  • current_spread – dI / I where dI is the 1/e half width

    • +
+
+
+
+ +
+ +
+
+class parakeet.microscope.Microscope(model: ~parakeet.config.MicroscopeModel | None = None, beam: ~parakeet.beam.Beam = <parakeet.beam.Beam object>, lens: ~parakeet.lens.Lens = <parakeet.lens.Lens object>, detector: ~parakeet.detector.Detector = <parakeet.detector.Detector object>, phase_plate: ~parakeet.microscope.PhasePlate = <parakeet.microscope.PhasePlate object>, objective_aperture_cutoff_freq=None)
+

A class to encapsulate a microscope

+
+
+__init__(model: ~parakeet.config.MicroscopeModel | None = None, beam: ~parakeet.beam.Beam = <parakeet.beam.Beam object>, lens: ~parakeet.lens.Lens = <parakeet.lens.Lens object>, detector: ~parakeet.detector.Detector = <parakeet.detector.Detector object>, phase_plate: ~parakeet.microscope.PhasePlate = <parakeet.microscope.PhasePlate object>, objective_aperture_cutoff_freq=None)
+

Initialise the detector

+
+
Parameters:
+
    +

  • model – The microscope model name

    • +

  • beam – The beam object

    • +

  • lens – The lens object

    • +

  • detector – The detector object

    • +

  • phase_plate – The phase plate

    • +
+
+
+
+ +
+
+property beam: Beam
+

The beam model

+
+ +
+
+property detector: Detector
+

The detector model

+
+ +
+
+property lens: Lens
+

The lens model

+
+ +
+
+property model: MicroscopeModel | None
+

The microscope model type

+
+ +
+
+property phase_plate: PhasePlate
+

Do we have a phase plate

+
+ +
+ +
+
+class parakeet.scan.Scan(image_number: ndarray | None = None, fraction_number: ndarray | None = None, axis: ndarray | None = None, angle: ndarray | None = None, shift: ndarray | None = None, shift_delta: ndarray | None = None, beam_tilt_theta: ndarray | None = None, beam_tilt_phi: ndarray | None = None, electrons_per_angstrom: ndarray | None = None, defocus_offset: ndarray | None = None, exposure_time: float = 1, is_uniform_angular_scan: bool = False)
+

A scan of angles around a single rotation axis.

+
+
+__init__(image_number: ndarray | None = None, fraction_number: ndarray | None = None, axis: ndarray | None = None, angle: ndarray | None = None, shift: ndarray | None = None, shift_delta: ndarray | None = None, beam_tilt_theta: ndarray | None = None, beam_tilt_phi: ndarray | None = None, electrons_per_angstrom: ndarray | None = None, defocus_offset: ndarray | None = None, exposure_time: float = 1, is_uniform_angular_scan: bool = False)
+

Initialise the scan

+
+ +
+
+property angles: ndarray
+

Get the angles

+
+ +
+
+property axes: ndarray
+

Get the axes

+
+ +
+
+property beam_tilt_phi: ndarray
+

Get the beam tilt phi angles

+
+ +
+
+property beam_tilt_theta: ndarray
+

Get the beam tilt theta angles

+
+ +
+
+property defocus_offset: ndarray
+

Get the defocus offset

+
+ +
+
+property electrons_per_angstrom: ndarray
+

Get the dose

+
+ +
+
+property euler_angles: ndarray
+

Euler angle representation of the orientations.

+

The Euler angles are intrinsic, right handed rotations around ZYZ. +This matches the convention used by XMIPP/RELION.

+
+ +
+
+property exposure_time: ndarray
+

Get the exposure times

+
+ +
+
+property fraction_number: ndarray
+

Get the movie fraction number

+
+ +
+
+property image_number: ndarray
+

Get the image number

+
+ +
+
+property orientation: ndarray
+

Get the orientations

+
+ +
+
+property position: ndarray
+

Get the positions

+
+ +
+
+property shift: ndarray
+

Get the shifts

+
+ +
+
+property shift_delta: ndarray
+

Get the shift deltas (drift)

+
+ +
+ +
+
+class parakeet.sample.Sample(filename=None, mode='r')
+

A class to hold the sample data

+
+
+__init__(filename=None, mode='r')
+

Initialise the class with a filename

+
+
Parameters:
+
    +

  • filename (str) – The filename

    • +

  • mode (str) – The open mode

    • +
+
+
+
+ +
+
+add_atoms(atoms)
+

Add some atoms

+
+
Parameters:
+

atoms (object) – The atom data to add to the sample

+
+
+
+ +
+
+add_molecule(atoms, positions, orientations, name=None)
+

Add a molecule.

+

This adds the atoms of each copy of the molecule but also stores the +molecule itself with the positions and orientations

+
+
Parameters:
+
    +

  • atoms (object) – The atom data

    • +

  • positions (list) – A list of positions

    • +

  • orientations (list) – A list of orientations

    • +

  • name (str) – The name of the molecule

    • +
+
+
+
+ +
+
+atoms_dataset_name(x)
+

Get the atom dataset name

+
+ +
+
+atoms_dataset_range(x0, x1)
+

Get the atom dataset range

+
+
Parameters:
+
    +

  • x0 (array) – The minimum coord

    • +

  • x1 (array) – The maximum coord

    • +
+
+
Yields:
+

tuple – The coordinates of the sub ranges

+
+
+
+ +
+
+atoms_dataset_range_3d(x0, x1)
+

Get the atom dataset range

+
+
Parameters:
+
    +

  • x0 (array) – The minimum coord

    • +

  • x1 (array) – The maximum coord

    • +
+
+
Yields:
+

tuple – The coordinates of the sub ranges

+
+
+
+ +
+
+property bounding_box
+

The bounding box

+
+
Returns:
+

lower, upper - the bounding box coordinates

+
+
Return type:
+

tuple

+
+
+
+ +
+
+property centre
+

The centre of the shape

+
+ +
+
+close()
+

Close the HDF5 file

+
+ +
+
+property containing_box
+

The box containing the sample

+
+ +
+
+del_atoms(deleter)
+

Delete atoms in the given range

+
+
Parameters:
+

deleter (func) – Check atoms and return only those we want to keep

+
+
+
+ +
+
+property dimensions
+

The dimensions of the bounding box

+
+
Returns:
+

The dimensions

+
+
Return type:
+

array

+
+
+
+ +
+
+get_atoms()
+

Get all the atoms

+
+
Returns:
+

The atom data

+
+
Return type:
+

object

+
+
+
+ +
+
+get_atoms_in_fov(x0, x1)
+

Get the subset of atoms within the field of view

+
+
Parameters:
+
    +

  • x0 (float) – The start of the z range

    • +

  • x1 (float) – The end of the z range

    • +
+
+
Returns:
+

The atom data

+
+
Return type:
+

object

+
+
+
+ +
+
+get_atoms_in_group(name)
+

Get the atoms in the group

+
+ +
+
+get_atoms_in_range(x0, x1, filter=None)
+

Get the subset of atoms within the field of view

+
+
Parameters:
+
    +

  • x0 (float) – The start of the z range

    • +

  • x1 (float) – The end of the z range

    • +

  • filter (func) – A function to filter the atoms

    • +
+
+
Returns:
+

The atom data

+
+
Return type:
+

object

+
+
+
+ +
+
+get_molecule(name)
+

Get the molcule data

+
+
Parameters:
+

name (str) – The molecule name

+
+
Returns:
+

The molecule data

+
+
Return type:
+

tuple (atoms, positions, orientations)

+
+
+
+ +
+
+identifier(name)
+

Get an identifier for the object

+
+ +
+
+info()
+

Get some sample info

+
+
Returns:
+

Some sample info

+
+
Return type:
+

str

+
+
+
+ +
+
+iter_atom_groups()
+

Iterate over the atom groups

+
+
Yields:
+

object – The atom group

+
+
+
+ +
+
+iter_atoms()
+

Iterate over the atoms

+
+
Yields:
+

object – The atom data

+
+
+
+ +
+
+iter_molecules()
+

Iterate over the molecules

+
+
Yields:
+

tuple (name, data) – The molecule data

+
+
+
+ +
+
+property molecules
+

The list of molecule names

+
+
Returns:
+

The list of molecule names

+
+
Return type:
+

list

+
+
+
+ +
+
+property number_of_atoms
+

Returns: +int: The number of atoms

+
+ +
+
+property number_of_molecular_models
+

The number of molecular models

+
+
Returns:
+

The number of molecular models

+
+
Return type:
+

int

+
+
+
+ +
+
+property number_of_molecules
+

The number of molecules

+
+
Returns:
+

The number of molcules

+
+
Return type:
+

int

+
+
+
+ +
+
+property shape
+

The ideal shape of the sample

+
+ +
+
+property shape_box
+

Return the shape box

+
+ +
+
+property shape_radius
+

Return a radius

+
+ +
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/configuration.html b/docs/configuration.html new file mode 100644 index 00000000..3f160208 --- /dev/null +++ b/docs/configuration.html @@ -0,0 +1,7138 @@ + + + + + + + + + Configuration — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Configuration

+
+

Definitions

+

Parakeet is configured via a YAML configuration file. The parameters of the +configuration file are defined below and additional example configuation files +can be seen at the bottom of the page.

+
+
$defs:
+
+
Auto:
+
+
const:
+

auto

+
+
description:
+

An enumeration just containing auto

+
+
enum:
+
    +

  • auto

    • +
+
+
title:
+

Auto

+
+
type:
+

string

+
+
+
+
Beam:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the beam

+
+
properties:
+
+
energy:
+
+
description:
+

The electron energy (keV)

+
+
title:
+

Energy

+
+
type:
+

number

+
+
+
+
energy_spread:
+
+
description:
+

The energy spread (dE/E)

+
+
title:
+

Energy Spread

+
+
type:
+

number

+
+
+
+
acceleration_voltage_spread:
+
+
description:
+

The acceleration voltage spread (dV/V)

+
+
title:
+

Acceleration Voltage Spread

+
+
type:
+

number

+
+
+
+
electrons_per_angstrom:
+
+
description:
+

The number of electrons per square angstrom. This is the dose per image (across all fractions).

+
+
title:
+

Electrons Per Angstrom

+
+
type:
+

number

+
+
+
+
illumination_semiangle:
+
+
description:
+

The illumination semiangle (mrad).

+
+
title:
+

Illumination Semiangle

+
+
type:
+

number

+
+
+
+
theta:
+
+
description:
+

The beam tilt theta angle (deg)

+
+
title:
+

Theta

+
+
type:
+

number

+
+
+
+
phi:
+
+
description:
+

The beam tilt phi angle (deg)

+
+
title:
+

Phi

+
+
type:
+

number

+
+
+
+
incident_wave:
+
+
anyOf:
+
    +
  • +
    type:
    +

    string

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The filename of a custom input wave function. The default is a flat field.

+
+
title:
+

Incident Wave

+
+
+
+
+
+
title:
+

Beam

+
+
type:
+

object

+
+
+
+
CoordinateFile:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a local coordinate file

+
+
properties:
+
+
filename:
+
+
anyOf:
+
    +
  • +
    type:
    +

    string

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The filename of the atomic coordinates to use (*.pdb, *.cif)

+
+
title:
+

Filename

+
+
+
+
recentre:
+
+
description:
+

Recentre the coordinates

+
+
title:
+

Recentre

+
+
type:
+

boolean

+
+
+
+
scale:
+
+
description:
+

Scale the coordinates x’ = x * scale

+
+
title:
+

Scale

+
+
type:
+

number

+
+
+
+
position:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The model position (A, A, A). If recentre if set then the model will be centred on the given position. If recentre if not set then the model will be translated by the given position.

+
+
examples:
+
    +

  • position: null # Assign [0, 0, 0] position

    • +

  • position: [1, 2, 3] # Assign known position

    • +
+
+
title:
+

Position

+
+
+
+
orientation:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The model orientation defined as a rotation vector where the direction of the vector gives the rotation axis and the magnitude of the vector gives the rotation angle in radians. Setting this to null or an empty list will cause parakeet to give a zero orientation

+
+
examples:
+
    +

  • orienation: null # Assign [0, 0, 0] orienation

    • +

  • orienation: [1, 2, 3] # Assign known orienation

    • +
+
+
title:
+

Orientation

+
+
+
+
+
+
title:
+

CoordinateFile

+
+
type:
+

object

+
+
+
+
Cube:
+
+
additionalProperties:
+

False

+
+
description:
+

A model of a cubic sample shape

+
+
properties:
+
+
length:
+
+
description:
+

The cube side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Cube

+
+
type:
+

object

+
+
+
+
Cuboid:
+
+
additionalProperties:
+

False

+
+
description:
+

A model of a cuboid sample shape

+
+
properties:
+
+
length_x:
+
+
description:
+

The cuboid X side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length X

+
+
type:
+

number

+
+
+
+
length_y:
+
+
description:
+

The cuboid Y side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length Y

+
+
type:
+

number

+
+
+
+
length_z:
+
+
description:
+

The cuboid Z side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length Z

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Cuboid

+
+
type:
+

object

+
+
+
+
Cylinder:
+
+
additionalProperties:
+

False

+
+
description:
+

A model of a cylindrical sample shape

+
+
properties:
+
+
length:
+
+
description:
+

The cylinder length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length

+
+
type:
+

number

+
+
+
+
radius:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The cylinder radius (A)

+
+
gt:
+

0

+
+
title:
+

Radius

+
+
+
+
axis:
+
+
description:
+

The axis of the cylinder

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Axis

+
+
type:
+

array

+
+
+
+
offset_x:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The x offset as a function of cylinder y position

+
+
title:
+

Offset X

+
+
+
+
offset_z:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The z offset as a function of cylinder y position

+
+
title:
+

Offset Z

+
+
+
+
+
+
title:
+

Cylinder

+
+
type:
+

object

+
+
+
+
Detector:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the detector

+
+
properties:
+
+
nx:
+
+
description:
+

The number of pixels in X

+
+
title:
+

Nx

+
+
type:
+

integer

+
+
+
+
ny:
+
+
description:
+

The number of pixels in Y

+
+
title:
+

Ny

+
+
type:
+

integer

+
+
+
+
pixel_size:
+
+
description:
+

The pixel size (A)

+
+
title:
+

Pixel Size

+
+
type:
+

number

+
+
+
+
dqe:
+
+
description:
+

Use the DQE model (True/False)

+
+
title:
+

Dqe

+
+
type:
+

boolean

+
+
+
+
origin:
+
+
description:
+

The origin of the detector in lab space(A,A)

+
+
maxItems:
+

2

+
+
minItems:
+

2

+
+
prefixItems:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
+
+
title:
+

Origin

+
+
type:
+

array

+
+
+
+
+
+
title:
+

Detector

+
+
type:
+

object

+
+
+
+
Device:
+
+
description:
+

An enumeration to set whether to run on the GPU or CPU

+
+
enum:
+
    +

  • gpu

    • +

  • cpu

    • +
+
+
title:
+

Device

+
+
type:
+

string

+
+
+
+
Drift:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the beam drift

+
+
properties:
+
+
x:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The model for the x drift a + b*theta**4 (A)

+
+
title:
+

X

+
+
+
+
y:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The model for the y drift a + b*theta**4 (A)

+
+
title:
+

Y

+
+
+
+
z:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The model for the z drift a + b*theta**4 (A)

+
+
title:
+

Z

+
+
+
+
+
+
title:
+

Drift

+
+
type:
+

object

+
+
+
+
Ice:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a uniform random atomic ice model. If generate is True +then generate random water positions with a given density. It is usually +better to use the Gaussian Random Field (GRF) ice model which can be set in +the simulation model.

+
+
properties:
+
+
generate:
+
+
description:
+

Generate the atomic ice model (True/False)

+
+
title:
+

Generate

+
+
type:
+

boolean

+
+
+
+
density:
+
+
description:
+

The density of the ice (Kg/m3)

+
+
title:
+

Density

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Ice

+
+
type:
+

object

+
+
+
+
IceParameters:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the ice parameters

+
+
properties:
+
+
m1:
+
+
description:
+

The mean of gaussian 1

+
+
title:
+

M1

+
+
type:
+

number

+
+
+
+
m2:
+
+
description:
+

The mean of gaussian 2

+
+
title:
+

M2

+
+
type:
+

number

+
+
+
+
s1:
+
+
description:
+

The standard deviation of gaussian 1

+
+
title:
+

S1

+
+
type:
+

number

+
+
+
+
s2:
+
+
description:
+

The standard deviation of gaussian 2

+
+
title:
+

S2

+
+
type:
+

number

+
+
+
+
a1:
+
+
description:
+

The amplitude of gaussian 1

+
+
title:
+

A1

+
+
type:
+

number

+
+
+
+
a2:
+
+
description:
+

The amplitude of gaussian 2

+
+
title:
+

A2

+
+
type:
+

number

+
+
+
+
density:
+
+
description:
+

The density of the ice (g/cm^3)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Density

+
+
type:
+

number

+
+
+
+
+
+
title:
+

IceParameters

+
+
type:
+

object

+
+
+
+
InelasticModel:
+
+
description:
+

A model to describe the inelastic scattering mode

+
+
enum:
+
    +

  • zero_loss

    • +

  • mp_loss

    • +

  • unfiltered

    • +

  • cc_corrected

    • +
+
+
title:
+

InelasticModel

+
+
type:
+

string

+
+
+
+
Lens:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the objective lens

+
+
properties:
+
+
c_10:
+
+
description:
+

The defocus (A). Negative is underfocus.

+
+
title:
+

C 10

+
+
type:
+

number

+
+
+
+
c_12:
+
+
description:
+

The 2-fold astigmatism (A)

+
+
title:
+

C 12

+
+
type:
+

number

+
+
+
+
phi_12:
+
+
description:
+

The Azimuthal angle of 2-fold astigmatism (rad)

+
+
title:
+

Phi 12

+
+
type:
+

number

+
+
+
+
c_21:
+
+
description:
+

The Axial coma (A)

+
+
title:
+

C 21

+
+
type:
+

number

+
+
+
+
phi_21:
+
+
description:
+

The Azimuthal angle of axial coma (rad)

+
+
title:
+

Phi 21

+
+
type:
+

number

+
+
+
+
c_23:
+
+
description:
+

The 3-fold astigmatism (A)

+
+
title:
+

C 23

+
+
type:
+

number

+
+
+
+
phi_23:
+
+
description:
+

The Azimuthal angle of 3-fold astigmatism (rad)

+
+
title:
+

Phi 23

+
+
type:
+

number

+
+
+
+
c_30:
+
+
description:
+

The 3rd order spherical aberration (mm)

+
+
title:
+

C 30

+
+
type:
+

number

+
+
+
+
c_32:
+
+
description:
+

The Axial star aberration (A)

+
+
title:
+

C 32

+
+
type:
+

number

+
+
+
+
phi_32:
+
+
description:
+

The Azimuthal angle of axial star aberration (rad)

+
+
title:
+

Phi 32

+
+
type:
+

number

+
+
+
+
c_34:
+
+
description:
+

The 4-fold astigmatism (A)

+
+
title:
+

C 34

+
+
type:
+

number

+
+
+
+
phi_34:
+
+
description:
+

The Azimuthal angle of 4-fold astigmatism (rad)

+
+
title:
+

Phi 34

+
+
type:
+

number

+
+
+
+
c_41:
+
+
description:
+

The 4th order axial coma (A)

+
+
title:
+

C 41

+
+
type:
+

number

+
+
+
+
phi_41:
+
+
description:
+

The Azimuthal angle of 4th order axial coma (rad)

+
+
title:
+

Phi 41

+
+
type:
+

number

+
+
+
+
c_43:
+
+
description:
+

The 3-lobe aberration (A)

+
+
title:
+

C 43

+
+
type:
+

number

+
+
+
+
phi_43:
+
+
description:
+

The Azimuthal angle of 3-lobe aberration (rad)

+
+
title:
+

Phi 43

+
+
type:
+

number

+
+
+
+
c_45:
+
+
description:
+

The 5-fold astigmatism (A)

+
+
title:
+

C 45

+
+
type:
+

number

+
+
+
+
phi_45:
+
+
description:
+

The Azimuthal angle of 5-fold astigmatism (rad)

+
+
title:
+

Phi 45

+
+
type:
+

number

+
+
+
+
c_50:
+
+
description:
+

The 5th order spherical aberration (A)

+
+
title:
+

C 50

+
+
type:
+

number

+
+
+
+
c_52:
+
+
description:
+

The 5th order axial star aberration (A)

+
+
title:
+

C 52

+
+
type:
+

number

+
+
+
+
phi_52:
+
+
description:
+

The Azimuthal angle of 5th order axial star aberration (rad)

+
+
title:
+

Phi 52

+
+
type:
+

number

+
+
+
+
c_54:
+
+
description:
+

The 5th order rosette aberration (A)

+
+
title:
+

C 54

+
+
type:
+

number

+
+
+
+
phi_54:
+
+
description:
+

The Azimuthal angle of 5th order rosette aberration (rad)

+
+
title:
+

Phi 54

+
+
type:
+

number

+
+
+
+
c_56:
+
+
description:
+

The 6-fold astigmatism (A)

+
+
title:
+

C 56

+
+
type:
+

number

+
+
+
+
phi_56:
+
+
description:
+

The Azimuthal angle of 6-fold astigmatism (rad)

+
+
title:
+

Phi 56

+
+
type:
+

number

+
+
+
+
inner_aper_ang:
+
+
description:
+

The inner aperture angle

+
+
title:
+

Inner Aper Ang

+
+
type:
+

number

+
+
+
+
outer_aper_ang:
+
+
description:
+

The outer aperture angle

+
+
title:
+

Outer Aper Ang

+
+
type:
+

number

+
+
+
+
c_c:
+
+
description:
+

The chromatic aberration (mm)

+
+
title:
+

C C

+
+
type:
+

number

+
+
+
+
current_spread:
+
+
description:
+

The current spread (dI/I)

+
+
title:
+

Current Spread

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Lens

+
+
type:
+

object

+
+
+
+
LocalMolecule:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a local molecule and its instances

+
+
properties:
+
+
filename:
+
+
description:
+

The filename of the atomic coordinates to use (*.pdb, *.cif)

+
+
title:
+

Filename

+
+
type:
+

string

+
+
+
+
instances:
+
+
anyOf:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    items:
    +
    +
    $ref:
    +

    MoleculePose

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The instances of the molecule to put into the sample model. This field can be set as either an integer or a list of MoleculePose objects. If it is set to an integer == 1 then the molecule will be positioned in the centre of the sample volume; any other integer will result in the molecules being positioned at random positions and orientations in the volume. If a list of MoleculePose objects is given then an arbitrary selection of random and assigned positions and poses can be set

+
+
examples:
+
    +

  • instances: 1 # Position 1 molecule at the centre of the sample volume

    • +

  • instances: 10 # Position 10 molecules at random

    • +

  • instances: [ { position: [1, 2, 3], orientation: [4, 5, 6] } ]

    • +
+
+
title:
+

Instances

+
+
+
+
+
+
required:
+
    +

  • filename

    • +
+
+
title:
+

LocalMolecule

+
+
type:
+

object

+
+
+
+
MPLPosition:
+
+
description:
+

A model to describe the MPL position mode

+
+
enum:
+
    +

  • peak

    • +

  • optimal

    • +
+
+
title:
+

MPLPosition

+
+
type:
+

string

+
+
+
+
Microscope:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the microscope

+
+
properties:
+
+
model:
+
+
anyOf:
+
+
+
description:
+

Use parameters for a given microscope model

+
+
+
+
beam:
+
+
$ref:
+

Beam

+
+
description:
+

The beam model parameters

+
+
+
+
lens:
+
+
$ref:
+

Lens

+
+
description:
+

The lens model parameters

+
+
+
+
phase_plate:
+
+
$ref:
+

PhasePlate

+
+
description:
+

The phase plate parameters

+
+
+
+
objective_aperture_cutoff_freq:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The objective aperture cutoff frequency (1/A)

+
+
title:
+

Objective Aperture Cutoff Freq

+
+
+
+
detector:
+
+
$ref:
+

Detector

+
+
description:
+

The detector model parameters

+
+
+
+
+
+
title:
+

Microscope

+
+
type:
+

object

+
+
+
+
MicroscopeModel:
+
+
description:
+

An enumeration to describe the microscope model

+
+
enum:
+
    +

  • krios

    • +

  • talos

    • +
+
+
title:
+

MicroscopeModel

+
+
type:
+

string

+
+
+
+
MoleculePose:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a molecule position and orientation

+
+
properties:
+
+
position:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The molecule position (A, A, A). Setting this to null or an empty list will cause parakeet to give a random position. The position is given in [x y z] order.

+
+
examples:
+
    +

  • position: null # Assign random position

    • +

  • position: [] # Assign random position

    • +

  • position: [1, 2, 3] # Assign known position

    • +
+
+
title:
+

Position

+
+
+
+
orientation:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The molecule orientation defined as a rotation vector where the direction of the vector gives the rotation axis and the magnitude of the vector gives the rotation angle in radians. Setting this to null or an empty list will cause parakeet to give a random orientation. The axis is given in [x, y, z] order.

+
+
examples:
+
    +

  • orienation: null # Assign random orienation

    • +

  • orienation: [] # Assign random orienation

    • +

  • orienation: [1, 2, 3] # Assign known orienation

    • +
+
+
title:
+

Orientation

+
+
+
+
+
+
title:
+

MoleculePose

+
+
type:
+

object

+
+
+
+
Molecules:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the molecules to add to the sample

+
+
properties:
+
+
local:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    $ref:
    +

    LocalMolecule

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The local molecules to include in the sample model

+
+
title:
+

Local

+
+
+
+
pdb:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    $ref:
    +

    PDBMolecule

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The PDB molecules to include in the sample model

+
+
title:
+

Pdb

+
+
+
+
+
+
title:
+

Molecules

+
+
type:
+

object

+
+
+
+
Multiprocessing:
+
+
additionalProperties:
+

False

+
+
description:
+

The multiprocessing parameters

+
+
properties:
+
+
device:
+
+
$ref:
+

Device

+
+
description:
+

The device to use (cpu or gpu)

+
+
+
+
nproc:
+
+
description:
+

The number of processes

+
+
exclusiveMinimum:
+

0

+
+
title:
+

Nproc

+
+
type:
+

integer

+
+
+
+
gpu_id:
+
+
description:
+

The GPU id for each thread

+
+
items:
+
+
type:
+

integer

+
+
+
+
title:
+

Gpu Id

+
+
type:
+

array

+
+
+
+
+
+
title:
+

Multiprocessing

+
+
type:
+

object

+
+
+
+
PDBMolecule:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a PDB molecule and its instances

+
+
properties:
+
+
id:
+
+
description:
+

The PDB ID of the atomic coordinates to use (*.pdb, *.cif)

+
+
title:
+

Id

+
+
type:
+

string

+
+
+
+
instances:
+
+
anyOf:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    items:
    +
    +
    $ref:
    +

    MoleculePose

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The instances of the molecule to put into the sample model. This field can be set as either an integer or a list of MoleculePose objects. If it is set to an integer == 1 then the molecule will be positioned in the centre of the sample volume; any other integer will result in the molecules being positioned at random positions and orientations in the volume. If a list of MoleculePose objects is given then an arbitrary selection of random and assigned positions and poses can be set

+
+
examples:
+
    +

  • instances: 1 # Position 1 molecule at the centre of the sample volume

    • +

  • instances: 10 # Position 10 molecules at random

    • +

  • instances: [ { position: [1, 2, 3], orientation: [4, 5, 6] } ]

    • +
+
+
title:
+

Instances

+
+
+
+
+
+
required:
+
    +

  • id

    • +
+
+
title:
+

PDBMolecule

+
+
type:
+

object

+
+
+
+
PhasePlate:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the phase plate

+
+
properties:
+
+
use:
+
+
description:
+

Use the phase plate

+
+
title:
+

Use

+
+
type:
+

boolean

+
+
+
+
phase_shift:
+
+
description:
+

The phase shift (degrees)

+
+
title:
+

Phase Shift

+
+
type:
+

number

+
+
+
+
radius:
+
+
description:
+

The spot radius (1/A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Radius

+
+
type:
+

number

+
+
+
+
+
+
title:
+

PhasePlate

+
+
type:
+

object

+
+
+
+
Sample:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the sample

+
+
properties:
+
+
shape:
+
+
$ref:
+

Shape

+
+
description:
+

The shape parameters of the sample

+
+
+
+
box:
+
+
description:
+

The sample box (A, A, A)

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Box

+
+
type:
+

array

+
+
+
+
centre:
+
+
description:
+

The centre of rotation (A, A, A)

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Centre

+
+
type:
+

array

+
+
+
+
coords:
+
+
anyOf:
+
+
+
description:
+

Coordinates to initialise the sample

+
+
+
+
molecules:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Molecules

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The molecules to include in the sample model

+
+
+
+
ice:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Ice

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The atomic ice model parameters.

+
+
+
+
sputter:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Sputter

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The sputter coating model parameters.

+
+
+
+
motion:
+
+
anyOf:
+
+
+
description:
+

The sample motion parameters

+
+
+
+
+
+
title:
+

Sample

+
+
type:
+

object

+
+
+
+
SampleMotion:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe sample motion using the viscek model

+
+
properties:
+
+
interaction_range:
+
+
description:
+

The interaction range (A)

+
+
title:
+

Interaction Range

+
+
type:
+

number

+
+
+
+
velocity:
+
+
description:
+

The particle velocity (A / fraction)

+
+
title:
+

Velocity

+
+
type:
+

number

+
+
+
+
noise_magnitude:
+
+
description:
+

The magnitude of the direction noise (degrees)

+
+
title:
+

Noise Magnitude

+
+
type:
+

number

+
+
+
+
+
+
title:
+

SampleMotion

+
+
type:
+

object

+
+
+
+
Scan:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the scan

+
+
properties:
+
+
mode:
+
+
$ref:
+

ScanMode

+
+
description:
+

Set the scan mode

+
+
+
+
axis:
+
+
description:
+

The scan axis vector

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Axis

+
+
type:
+

array

+
+
+
+
start_angle:
+
+
description:
+

The start angle for the rotation (deg)

+
+
title:
+

Start Angle

+
+
type:
+

number

+
+
+
+
step_angle:
+
+
description:
+

The step angle for the rotation (deg)

+
+
title:
+

Step Angle

+
+
type:
+

number

+
+
+
+
start_pos:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The start position for a translational scan (A)

+
+
title:
+

Start Pos

+
+
+
+
step_pos:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    $ref:
    +

    Auto

    +
    +
    +
    • +
+
+
description:
+

The step distance for a translational scan (A)

+
+
title:
+

Step Pos

+
+
+
+
num_images:
+
+
anyOf:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      integer

      +
      +
      +
      • +
    • +
      type:
      +

      integer

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The number of images to simulate. For a tilt series this is the number of tilt steps. If num_fractions is also set to something other than 1, then there will be num_fractions number of ‘movie frames’ per ‘image’

+
+
title:
+

Num Images

+
+
+
+
num_fractions:
+
+
description:
+

The number of movie frames. This refers to the frames of the micrograph ‘movies’. For a tilt series, all these images will be at the same step and the dose for a ‘single image’ will be fractionated over these image frames

+
+
title:
+

Num Fractions

+
+
type:
+

integer

+
+
+
+
num_nhelix:
+
+
description:
+

The number of scans in an n-helix

+
+
title:
+

Num Nhelix

+
+
type:
+

integer

+
+
+
+
exposure_time:
+
+
description:
+

The exposure time per image (s)

+
+
title:
+

Exposure Time

+
+
type:
+

number

+
+
+
+
angles:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of angles to use (deg). This field is used when the modeis set to ‘manual’ or ‘beam tilt’.

+
+
title:
+

Angles

+
+
+
+
positions:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    items:
    +
    +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of positions to use (A). This field is used when the modeis set to ‘manual’ or ‘beam tilt’. Each element in the list can either be a single value in which case the position is specified along the rotation axis, or can be two values in which case the position is specified in X and Y.

+
+
title:
+

Positions

+
+
+
+
defocus_offset:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of defoci to use (A). This field is used when the modeis set to ‘manual’ or ‘single_particle’

+
+
title:
+

Defocus Offset

+
+
+
+
theta:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of theta angles to use (mrad) for the beam tilt.This must either be the same length as phi or a scalar

+
+
title:
+

Theta

+
+
+
+
phi:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of phi angles to use (mrad) for the beam tilt.This must either be the same length as theta or a scalar

+
+
title:
+

Phi

+
+
+
+
drift:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Drift

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The drift model parameters

+
+
+
+
+
+
title:
+

Scan

+
+
type:
+

object

+
+
+
+
ScanMode:
+
+
description:
+

An enumeration to describe the scan mode

+
+
enum:
+
    +

  • manual

    • +

  • still

    • +

  • tilt_series

    • +

  • dose_symmetric

    • +

  • single_particle

    • +

  • helical_scan

    • +

  • nhelix

    • +

  • beam_tilt

    • +

  • grid_scan

    • +
+
+
title:
+

ScanMode

+
+
type:
+

string

+
+
+
+
Shape:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the sample shape

+
+
properties:
+
+
type:
+
+
$ref:
+

ShapeType

+
+
description:
+

The shape of the sample

+
+
+
+
cube:
+
+
$ref:
+

Cube

+
+
description:
+

The parameters of the cubic sample (only used if type == cube)

+
+
+
+
cuboid:
+
+
$ref:
+

Cuboid

+
+
description:
+

The parameters of the cuboid sample (only used if type == cuboid)

+
+
+
+
cylinder:
+
+
$ref:
+

Cylinder

+
+
description:
+

The parameters of the cylindrical sample (only used if type == cylinder)

+
+
+
+
margin:
+
+
description:
+

The shape margin used to define how close to the edges particles should be placed (A)

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Margin

+
+
type:
+

array

+
+
+
+
+
+
title:
+

Shape

+
+
type:
+

object

+
+
+
+
ShapeType:
+
+
description:
+

An enumeration of sample shape types

+
+
enum:
+
    +

  • cube

    • +

  • cuboid

    • +

  • cylinder

    • +
+
+
title:
+

ShapeType

+
+
type:
+

string

+
+
+
+
Simulation:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the simulation parameters

+
+
properties:
+
+
slice_thickness:
+
+
description:
+

The multislice thickness (A)

+
+
title:
+

Slice Thickness

+
+
type:
+

number

+
+
+
+
margin:
+
+
description:
+

The margin around the image

+
+
title:
+

Margin

+
+
type:
+

integer

+
+
+
+
padding:
+
+
description:
+

Additional padding

+
+
title:
+

Padding

+
+
type:
+

integer

+
+
+
+
division_thickness:
+
+
description:
+

Deprecated

+
+
title:
+

Division Thickness

+
+
type:
+

integer

+
+
+
+
ice:
+
+
description:
+

Use the Gaussian Random Field ice model (True/False)

+
+
title:
+

Ice

+
+
type:
+

boolean

+
+
+
+
ice_parameters:
+
+
$ref:
+

IceParameters

+
+
description:
+

The parameters for the GRF ice model

+
+
+
+
radiation_damage_model:
+
+
description:
+

Use the radiation damage model (True/False)

+
+
title:
+

Radiation Damage Model

+
+
type:
+

boolean

+
+
+
+
inelastic_model:
+
+
anyOf:
+
+
+
description:
+

The inelastic model parameters

+
+
+
+
mp_loss_width:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The MPL energy filter width

+
+
title:
+

Mp Loss Width

+
+
+
+
mp_loss_position:
+
+
$ref:
+

MPLPosition

+
+
description:
+

The MPL energy filter position

+
+
+
+
sensitivity_coefficient:
+
+
description:
+

The radiation damage model sensitivity coefficient. This value relates the value of an isotropic B factor to the number of incident electrons. Typical values for this (calibrated from X-ray and EM data) range between 0.02 and 0.08 where a higher value will result in a larger B factor.

+
+
title:
+

Sensitivity Coefficient

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Simulation

+
+
type:
+

object

+
+
+
+
Sputter:
+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a sputter coating to the sample

+
+
properties:
+
+
element:
+
+
description:
+

The symbol of the atom for the sputter coating material

+
+
title:
+

Element

+
+
type:
+

string

+
+
+
+
thickness:
+
+
description:
+

The thickness of the sputter coating (A)

+
+
title:
+

Thickness

+
+
type:
+

number

+
+
+
+
+
+
required:
+
    +

  • element

    • +

  • thickness

    • +
+
+
title:
+

Sputter

+
+
type:
+

object

+
+
+
+
+
+
additionalProperties:
+

False

+
+
description:
+

The Parakeet configuration parameters

+
+
properties:
+
+
sample:
+
+
$ref:
+

Sample

+
+
description:
+

The sample parameters

+
+
+
+
microscope:
+
+
$ref:
+

Microscope

+
+
description:
+

The microscope parameters

+
+
+
+
scan:
+
+
$ref:
+

Scan

+
+
description:
+

The scan parameters

+
+
+
+
simulation:
+
+
$ref:
+

Simulation

+
+
description:
+

The simulation parameters

+
+
+
+
multiprocessing:
+
+
$ref:
+

Multiprocessing

+
+
+
+
+
+
title:
+

Config

+
+
type:
+

object

+
+
+

+

Auto

+
+
const:
+

auto

+
+
description:
+

An enumeration just containing auto

+
+
enum:
+
    +

  • auto

    • +
+
+
title:
+

Auto

+
+
type:
+

string

+
+
+
+
+

Beam

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the beam

+
+
properties:
+
+
energy:
+
+
description:
+

The electron energy (keV)

+
+
title:
+

Energy

+
+
type:
+

number

+
+
+
+
energy_spread:
+
+
description:
+

The energy spread (dE/E)

+
+
title:
+

Energy Spread

+
+
type:
+

number

+
+
+
+
acceleration_voltage_spread:
+
+
description:
+

The acceleration voltage spread (dV/V)

+
+
title:
+

Acceleration Voltage Spread

+
+
type:
+

number

+
+
+
+
electrons_per_angstrom:
+
+
description:
+

The number of electrons per square angstrom. This is the dose per image (across all fractions).

+
+
title:
+

Electrons Per Angstrom

+
+
type:
+

number

+
+
+
+
illumination_semiangle:
+
+
description:
+

The illumination semiangle (mrad).

+
+
title:
+

Illumination Semiangle

+
+
type:
+

number

+
+
+
+
theta:
+
+
description:
+

The beam tilt theta angle (deg)

+
+
title:
+

Theta

+
+
type:
+

number

+
+
+
+
phi:
+
+
description:
+

The beam tilt phi angle (deg)

+
+
title:
+

Phi

+
+
type:
+

number

+
+
+
+
incident_wave:
+
+
anyOf:
+
    +
  • +
    type:
    +

    string

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The filename of a custom input wave function. The default is a flat field.

+
+
title:
+

Incident Wave

+
+
+
+
+
+
title:
+

Beam

+
+
type:
+

object

+
+
+
+
+

CoordinateFile

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a local coordinate file

+
+
properties:
+
+
filename:
+
+
anyOf:
+
    +
  • +
    type:
    +

    string

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The filename of the atomic coordinates to use (*.pdb, *.cif)

+
+
title:
+

Filename

+
+
+
+
recentre:
+
+
description:
+

Recentre the coordinates

+
+
title:
+

Recentre

+
+
type:
+

boolean

+
+
+
+
scale:
+
+
description:
+

Scale the coordinates x’ = x * scale

+
+
title:
+

Scale

+
+
type:
+

number

+
+
+
+
position:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The model position (A, A, A). If recentre if set then the model will be centred on the given position. If recentre if not set then the model will be translated by the given position.

+
+
examples:
+
    +

  • position: null # Assign [0, 0, 0] position

    • +

  • position: [1, 2, 3] # Assign known position

    • +
+
+
title:
+

Position

+
+
+
+
orientation:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The model orientation defined as a rotation vector where the direction of the vector gives the rotation axis and the magnitude of the vector gives the rotation angle in radians. Setting this to null or an empty list will cause parakeet to give a zero orientation

+
+
examples:
+
    +

  • orienation: null # Assign [0, 0, 0] orienation

    • +

  • orienation: [1, 2, 3] # Assign known orienation

    • +
+
+
title:
+

Orientation

+
+
+
+
+
+
title:
+

CoordinateFile

+
+
type:
+

object

+
+
+
+
+

Cube

+
+
additionalProperties:
+

False

+
+
description:
+

A model of a cubic sample shape

+
+
properties:
+
+
length:
+
+
description:
+

The cube side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Cube

+
+
type:
+

object

+
+
+
+
+

Cuboid

+
+
additionalProperties:
+

False

+
+
description:
+

A model of a cuboid sample shape

+
+
properties:
+
+
length_x:
+
+
description:
+

The cuboid X side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length X

+
+
type:
+

number

+
+
+
+
length_y:
+
+
description:
+

The cuboid Y side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length Y

+
+
type:
+

number

+
+
+
+
length_z:
+
+
description:
+

The cuboid Z side length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length Z

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Cuboid

+
+
type:
+

object

+
+
+
+
+

Cylinder

+
+
additionalProperties:
+

False

+
+
description:
+

A model of a cylindrical sample shape

+
+
properties:
+
+
length:
+
+
description:
+

The cylinder length (A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Length

+
+
type:
+

number

+
+
+
+
radius:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The cylinder radius (A)

+
+
gt:
+

0

+
+
title:
+

Radius

+
+
+
+
axis:
+
+
description:
+

The axis of the cylinder

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Axis

+
+
type:
+

array

+
+
+
+
offset_x:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The x offset as a function of cylinder y position

+
+
title:
+

Offset X

+
+
+
+
offset_z:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The z offset as a function of cylinder y position

+
+
title:
+

Offset Z

+
+
+
+
+
+
title:
+

Cylinder

+
+
type:
+

object

+
+
+
+
+

Detector

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the detector

+
+
properties:
+
+
nx:
+
+
description:
+

The number of pixels in X

+
+
title:
+

Nx

+
+
type:
+

integer

+
+
+
+
ny:
+
+
description:
+

The number of pixels in Y

+
+
title:
+

Ny

+
+
type:
+

integer

+
+
+
+
pixel_size:
+
+
description:
+

The pixel size (A)

+
+
title:
+

Pixel Size

+
+
type:
+

number

+
+
+
+
dqe:
+
+
description:
+

Use the DQE model (True/False)

+
+
title:
+

Dqe

+
+
type:
+

boolean

+
+
+
+
origin:
+
+
description:
+

The origin of the detector in lab space(A,A)

+
+
maxItems:
+

2

+
+
minItems:
+

2

+
+
prefixItems:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
+
+
title:
+

Origin

+
+
type:
+

array

+
+
+
+
+
+
title:
+

Detector

+
+
type:
+

object

+
+
+
+
+

Device

+
+
description:
+

An enumeration to set whether to run on the GPU or CPU

+
+
enum:
+
    +

  • gpu

    • +

  • cpu

    • +
+
+
title:
+

Device

+
+
type:
+

string

+
+
+
+
+

Drift

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the beam drift

+
+
properties:
+
+
x:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The model for the x drift a + b*theta**4 (A)

+
+
title:
+

X

+
+
+
+
y:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The model for the y drift a + b*theta**4 (A)

+
+
title:
+

Y

+
+
+
+
z:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The model for the z drift a + b*theta**4 (A)

+
+
title:
+

Z

+
+
+
+
+
+
title:
+

Drift

+
+
type:
+

object

+
+
+
+
+

Ice

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a uniform random atomic ice model. If generate is True +then generate random water positions with a given density. It is usually +better to use the Gaussian Random Field (GRF) ice model which can be set in +the simulation model.

+
+
properties:
+
+
generate:
+
+
description:
+

Generate the atomic ice model (True/False)

+
+
title:
+

Generate

+
+
type:
+

boolean

+
+
+
+
density:
+
+
description:
+

The density of the ice (Kg/m3)

+
+
title:
+

Density

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Ice

+
+
type:
+

object

+
+
+
+
+

IceParameters

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the ice parameters

+
+
properties:
+
+
m1:
+
+
description:
+

The mean of gaussian 1

+
+
title:
+

M1

+
+
type:
+

number

+
+
+
+
m2:
+
+
description:
+

The mean of gaussian 2

+
+
title:
+

M2

+
+
type:
+

number

+
+
+
+
s1:
+
+
description:
+

The standard deviation of gaussian 1

+
+
title:
+

S1

+
+
type:
+

number

+
+
+
+
s2:
+
+
description:
+

The standard deviation of gaussian 2

+
+
title:
+

S2

+
+
type:
+

number

+
+
+
+
a1:
+
+
description:
+

The amplitude of gaussian 1

+
+
title:
+

A1

+
+
type:
+

number

+
+
+
+
a2:
+
+
description:
+

The amplitude of gaussian 2

+
+
title:
+

A2

+
+
type:
+

number

+
+
+
+
density:
+
+
description:
+

The density of the ice (g/cm^3)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Density

+
+
type:
+

number

+
+
+
+
+
+
title:
+

IceParameters

+
+
type:
+

object

+
+
+
+
+

InelasticModel

+
+
description:
+

A model to describe the inelastic scattering mode

+
+
enum:
+
    +

  • zero_loss

    • +

  • mp_loss

    • +

  • unfiltered

    • +

  • cc_corrected

    • +
+
+
title:
+

InelasticModel

+
+
type:
+

string

+
+
+
+
+

Lens

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the objective lens

+
+
properties:
+
+
c_10:
+
+
description:
+

The defocus (A). Negative is underfocus.

+
+
title:
+

C 10

+
+
type:
+

number

+
+
+
+
c_12:
+
+
description:
+

The 2-fold astigmatism (A)

+
+
title:
+

C 12

+
+
type:
+

number

+
+
+
+
phi_12:
+
+
description:
+

The Azimuthal angle of 2-fold astigmatism (rad)

+
+
title:
+

Phi 12

+
+
type:
+

number

+
+
+
+
c_21:
+
+
description:
+

The Axial coma (A)

+
+
title:
+

C 21

+
+
type:
+

number

+
+
+
+
phi_21:
+
+
description:
+

The Azimuthal angle of axial coma (rad)

+
+
title:
+

Phi 21

+
+
type:
+

number

+
+
+
+
c_23:
+
+
description:
+

The 3-fold astigmatism (A)

+
+
title:
+

C 23

+
+
type:
+

number

+
+
+
+
phi_23:
+
+
description:
+

The Azimuthal angle of 3-fold astigmatism (rad)

+
+
title:
+

Phi 23

+
+
type:
+

number

+
+
+
+
c_30:
+
+
description:
+

The 3rd order spherical aberration (mm)

+
+
title:
+

C 30

+
+
type:
+

number

+
+
+
+
c_32:
+
+
description:
+

The Axial star aberration (A)

+
+
title:
+

C 32

+
+
type:
+

number

+
+
+
+
phi_32:
+
+
description:
+

The Azimuthal angle of axial star aberration (rad)

+
+
title:
+

Phi 32

+
+
type:
+

number

+
+
+
+
c_34:
+
+
description:
+

The 4-fold astigmatism (A)

+
+
title:
+

C 34

+
+
type:
+

number

+
+
+
+
phi_34:
+
+
description:
+

The Azimuthal angle of 4-fold astigmatism (rad)

+
+
title:
+

Phi 34

+
+
type:
+

number

+
+
+
+
c_41:
+
+
description:
+

The 4th order axial coma (A)

+
+
title:
+

C 41

+
+
type:
+

number

+
+
+
+
phi_41:
+
+
description:
+

The Azimuthal angle of 4th order axial coma (rad)

+
+
title:
+

Phi 41

+
+
type:
+

number

+
+
+
+
c_43:
+
+
description:
+

The 3-lobe aberration (A)

+
+
title:
+

C 43

+
+
type:
+

number

+
+
+
+
phi_43:
+
+
description:
+

The Azimuthal angle of 3-lobe aberration (rad)

+
+
title:
+

Phi 43

+
+
type:
+

number

+
+
+
+
c_45:
+
+
description:
+

The 5-fold astigmatism (A)

+
+
title:
+

C 45

+
+
type:
+

number

+
+
+
+
phi_45:
+
+
description:
+

The Azimuthal angle of 5-fold astigmatism (rad)

+
+
title:
+

Phi 45

+
+
type:
+

number

+
+
+
+
c_50:
+
+
description:
+

The 5th order spherical aberration (A)

+
+
title:
+

C 50

+
+
type:
+

number

+
+
+
+
c_52:
+
+
description:
+

The 5th order axial star aberration (A)

+
+
title:
+

C 52

+
+
type:
+

number

+
+
+
+
phi_52:
+
+
description:
+

The Azimuthal angle of 5th order axial star aberration (rad)

+
+
title:
+

Phi 52

+
+
type:
+

number

+
+
+
+
c_54:
+
+
description:
+

The 5th order rosette aberration (A)

+
+
title:
+

C 54

+
+
type:
+

number

+
+
+
+
phi_54:
+
+
description:
+

The Azimuthal angle of 5th order rosette aberration (rad)

+
+
title:
+

Phi 54

+
+
type:
+

number

+
+
+
+
c_56:
+
+
description:
+

The 6-fold astigmatism (A)

+
+
title:
+

C 56

+
+
type:
+

number

+
+
+
+
phi_56:
+
+
description:
+

The Azimuthal angle of 6-fold astigmatism (rad)

+
+
title:
+

Phi 56

+
+
type:
+

number

+
+
+
+
inner_aper_ang:
+
+
description:
+

The inner aperture angle

+
+
title:
+

Inner Aper Ang

+
+
type:
+

number

+
+
+
+
outer_aper_ang:
+
+
description:
+

The outer aperture angle

+
+
title:
+

Outer Aper Ang

+
+
type:
+

number

+
+
+
+
c_c:
+
+
description:
+

The chromatic aberration (mm)

+
+
title:
+

C C

+
+
type:
+

number

+
+
+
+
current_spread:
+
+
description:
+

The current spread (dI/I)

+
+
title:
+

Current Spread

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Lens

+
+
type:
+

object

+
+
+
+
+

LocalMolecule

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a local molecule and its instances

+
+
properties:
+
+
filename:
+
+
description:
+

The filename of the atomic coordinates to use (*.pdb, *.cif)

+
+
title:
+

Filename

+
+
type:
+

string

+
+
+
+
instances:
+
+
anyOf:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    items:
    +
    +
    $ref:
    +

    MoleculePose

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The instances of the molecule to put into the sample model. This field can be set as either an integer or a list of MoleculePose objects. If it is set to an integer == 1 then the molecule will be positioned in the centre of the sample volume; any other integer will result in the molecules being positioned at random positions and orientations in the volume. If a list of MoleculePose objects is given then an arbitrary selection of random and assigned positions and poses can be set

+
+
examples:
+
    +

  • instances: 1 # Position 1 molecule at the centre of the sample volume

    • +

  • instances: 10 # Position 10 molecules at random

    • +

  • instances: [ { position: [1, 2, 3], orientation: [4, 5, 6] } ]

    • +
+
+
title:
+

Instances

+
+
+
+
+
+
required:
+
    +

  • filename

    • +
+
+
title:
+

LocalMolecule

+
+
type:
+

object

+
+
+
+
+

MPLPosition

+
+
description:
+

A model to describe the MPL position mode

+
+
enum:
+
    +

  • peak

    • +

  • optimal

    • +
+
+
title:
+

MPLPosition

+
+
type:
+

string

+
+
+
+
+

Microscope

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the microscope

+
+
properties:
+
+
model:
+
+
anyOf:
+
+
+
description:
+

Use parameters for a given microscope model

+
+
+
+
beam:
+
+
$ref:
+

Beam

+
+
description:
+

The beam model parameters

+
+
+
+
lens:
+
+
$ref:
+

Lens

+
+
description:
+

The lens model parameters

+
+
+
+
phase_plate:
+
+
$ref:
+

PhasePlate

+
+
description:
+

The phase plate parameters

+
+
+
+
objective_aperture_cutoff_freq:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The objective aperture cutoff frequency (1/A)

+
+
title:
+

Objective Aperture Cutoff Freq

+
+
+
+
detector:
+
+
$ref:
+

Detector

+
+
description:
+

The detector model parameters

+
+
+
+
+
+
title:
+

Microscope

+
+
type:
+

object

+
+
+
+
+

MicroscopeModel

+
+
description:
+

An enumeration to describe the microscope model

+
+
enum:
+
    +

  • krios

    • +

  • talos

    • +
+
+
title:
+

MicroscopeModel

+
+
type:
+

string

+
+
+
+
+

MoleculePose

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a molecule position and orientation

+
+
properties:
+
+
position:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The molecule position (A, A, A). Setting this to null or an empty list will cause parakeet to give a random position. The position is given in [x y z] order.

+
+
examples:
+
    +

  • position: null # Assign random position

    • +

  • position: [] # Assign random position

    • +

  • position: [1, 2, 3] # Assign known position

    • +
+
+
title:
+

Position

+
+
+
+
orientation:
+
+
anyOf:
+
    +
  • +
    maxItems:
    +

    3

    +
    +
    minItems:
    +

    3

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The molecule orientation defined as a rotation vector where the direction of the vector gives the rotation axis and the magnitude of the vector gives the rotation angle in radians. Setting this to null or an empty list will cause parakeet to give a random orientation. The axis is given in [x, y, z] order.

+
+
examples:
+
    +

  • orienation: null # Assign random orienation

    • +

  • orienation: [] # Assign random orienation

    • +

  • orienation: [1, 2, 3] # Assign known orienation

    • +
+
+
title:
+

Orientation

+
+
+
+
+
+
title:
+

MoleculePose

+
+
type:
+

object

+
+
+
+
+

Molecules

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the molecules to add to the sample

+
+
properties:
+
+
local:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    $ref:
    +

    LocalMolecule

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The local molecules to include in the sample model

+
+
title:
+

Local

+
+
+
+
pdb:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    $ref:
    +

    PDBMolecule

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The PDB molecules to include in the sample model

+
+
title:
+

Pdb

+
+
+
+
+
+
title:
+

Molecules

+
+
type:
+

object

+
+
+
+
+

Multiprocessing

+
+
additionalProperties:
+

False

+
+
description:
+

The multiprocessing parameters

+
+
properties:
+
+
device:
+
+
$ref:
+

Device

+
+
description:
+

The device to use (cpu or gpu)

+
+
+
+
nproc:
+
+
description:
+

The number of processes

+
+
exclusiveMinimum:
+

0

+
+
title:
+

Nproc

+
+
type:
+

integer

+
+
+
+
gpu_id:
+
+
description:
+

The GPU id for each thread

+
+
items:
+
+
type:
+

integer

+
+
+
+
title:
+

Gpu Id

+
+
type:
+

array

+
+
+
+
+
+
title:
+

Multiprocessing

+
+
type:
+

object

+
+
+
+
+

PDBMolecule

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a PDB molecule and its instances

+
+
properties:
+
+
id:
+
+
description:
+

The PDB ID of the atomic coordinates to use (*.pdb, *.cif)

+
+
title:
+

Id

+
+
type:
+

string

+
+
+
+
instances:
+
+
anyOf:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    items:
    +
    +
    $ref:
    +

    MoleculePose

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The instances of the molecule to put into the sample model. This field can be set as either an integer or a list of MoleculePose objects. If it is set to an integer == 1 then the molecule will be positioned in the centre of the sample volume; any other integer will result in the molecules being positioned at random positions and orientations in the volume. If a list of MoleculePose objects is given then an arbitrary selection of random and assigned positions and poses can be set

+
+
examples:
+
    +

  • instances: 1 # Position 1 molecule at the centre of the sample volume

    • +

  • instances: 10 # Position 10 molecules at random

    • +

  • instances: [ { position: [1, 2, 3], orientation: [4, 5, 6] } ]

    • +
+
+
title:
+

Instances

+
+
+
+
+
+
required:
+
    +

  • id

    • +
+
+
title:
+

PDBMolecule

+
+
type:
+

object

+
+
+
+
+

PhasePlate

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the phase plate

+
+
properties:
+
+
use:
+
+
description:
+

Use the phase plate

+
+
title:
+

Use

+
+
type:
+

boolean

+
+
+
+
phase_shift:
+
+
description:
+

The phase shift (degrees)

+
+
title:
+

Phase Shift

+
+
type:
+

number

+
+
+
+
radius:
+
+
description:
+

The spot radius (1/A)

+
+
exclusiveMinimum:
+

0.0

+
+
title:
+

Radius

+
+
type:
+

number

+
+
+
+
+
+
title:
+

PhasePlate

+
+
type:
+

object

+
+
+
+
+

Sample

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the sample

+
+
properties:
+
+
shape:
+
+
$ref:
+

Shape

+
+
description:
+

The shape parameters of the sample

+
+
+
+
box:
+
+
description:
+

The sample box (A, A, A)

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Box

+
+
type:
+

array

+
+
+
+
centre:
+
+
description:
+

The centre of rotation (A, A, A)

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Centre

+
+
type:
+

array

+
+
+
+
coords:
+
+
anyOf:
+
+
+
description:
+

Coordinates to initialise the sample

+
+
+
+
molecules:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Molecules

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The molecules to include in the sample model

+
+
+
+
ice:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Ice

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The atomic ice model parameters.

+
+
+
+
sputter:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Sputter

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The sputter coating model parameters.

+
+
+
+
motion:
+
+
anyOf:
+
+
+
description:
+

The sample motion parameters

+
+
+
+
+
+
title:
+

Sample

+
+
type:
+

object

+
+
+
+
+

SampleMotion

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe sample motion using the viscek model

+
+
properties:
+
+
interaction_range:
+
+
description:
+

The interaction range (A)

+
+
title:
+

Interaction Range

+
+
type:
+

number

+
+
+
+
velocity:
+
+
description:
+

The particle velocity (A / fraction)

+
+
title:
+

Velocity

+
+
type:
+

number

+
+
+
+
noise_magnitude:
+
+
description:
+

The magnitude of the direction noise (degrees)

+
+
title:
+

Noise Magnitude

+
+
type:
+

number

+
+
+
+
+
+
title:
+

SampleMotion

+
+
type:
+

object

+
+
+
+
+

Scan

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the scan

+
+
properties:
+
+
mode:
+
+
$ref:
+

ScanMode

+
+
description:
+

Set the scan mode

+
+
+
+
axis:
+
+
description:
+

The scan axis vector

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Axis

+
+
type:
+

array

+
+
+
+
start_angle:
+
+
description:
+

The start angle for the rotation (deg)

+
+
title:
+

Start Angle

+
+
type:
+

number

+
+
+
+
step_angle:
+
+
description:
+

The step angle for the rotation (deg)

+
+
title:
+

Step Angle

+
+
type:
+

number

+
+
+
+
start_pos:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The start position for a translational scan (A)

+
+
title:
+

Start Pos

+
+
+
+
step_pos:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    $ref:
    +

    Auto

    +
    +
    +
    • +
+
+
description:
+

The step distance for a translational scan (A)

+
+
title:
+

Step Pos

+
+
+
+
num_images:
+
+
anyOf:
+
    +
  • +
    type:
    +

    integer

    +
    +
    +
    • +
  • +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      integer

      +
      +
      +
      • +
    • +
      type:
      +

      integer

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
+
+
description:
+

The number of images to simulate. For a tilt series this is the number of tilt steps. If num_fractions is also set to something other than 1, then there will be num_fractions number of ‘movie frames’ per ‘image’

+
+
title:
+

Num Images

+
+
+
+
num_fractions:
+
+
description:
+

The number of movie frames. This refers to the frames of the micrograph ‘movies’. For a tilt series, all these images will be at the same step and the dose for a ‘single image’ will be fractionated over these image frames

+
+
title:
+

Num Fractions

+
+
type:
+

integer

+
+
+
+
num_nhelix:
+
+
description:
+

The number of scans in an n-helix

+
+
title:
+

Num Nhelix

+
+
type:
+

integer

+
+
+
+
exposure_time:
+
+
description:
+

The exposure time per image (s)

+
+
title:
+

Exposure Time

+
+
type:
+

number

+
+
+
+
angles:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of angles to use (deg). This field is used when the modeis set to ‘manual’ or ‘beam tilt’.

+
+
title:
+

Angles

+
+
+
+
positions:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    items:
    +
    +
    maxItems:
    +

    2

    +
    +
    minItems:
    +

    2

    +
    +
    prefixItems:
    +
      +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    • +
      type:
      +

      number

      +
      +
      +
      • +
    +
    +
    type:
    +

    array

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of positions to use (A). This field is used when the modeis set to ‘manual’ or ‘beam tilt’. Each element in the list can either be a single value in which case the position is specified along the rotation axis, or can be two values in which case the position is specified in X and Y.

+
+
title:
+

Positions

+
+
+
+
defocus_offset:
+
+
anyOf:
+
    +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of defoci to use (A). This field is used when the modeis set to ‘manual’ or ‘single_particle’

+
+
title:
+

Defocus Offset

+
+
+
+
theta:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of theta angles to use (mrad) for the beam tilt.This must either be the same length as phi or a scalar

+
+
title:
+

Theta

+
+
+
+
phi:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    items:
    +
    +
    type:
    +

    number

    +
    +
    +
    +
    type:
    +

    array

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The list of phi angles to use (mrad) for the beam tilt.This must either be the same length as theta or a scalar

+
+
title:
+

Phi

+
+
+
+
drift:
+
+
anyOf:
+
    +
  • +
    $ref:
    +

    Drift

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The drift model parameters

+
+
+
+
+
+
title:
+

Scan

+
+
type:
+

object

+
+
+
+
+

ScanMode

+
+
description:
+

An enumeration to describe the scan mode

+
+
enum:
+
    +

  • manual

    • +

  • still

    • +

  • tilt_series

    • +

  • dose_symmetric

    • +

  • single_particle

    • +

  • helical_scan

    • +

  • nhelix

    • +

  • beam_tilt

    • +

  • grid_scan

    • +
+
+
title:
+

ScanMode

+
+
type:
+

string

+
+
+
+
+

Shape

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the sample shape

+
+
properties:
+
+
type:
+
+
$ref:
+

ShapeType

+
+
description:
+

The shape of the sample

+
+
+
+
cube:
+
+
$ref:
+

Cube

+
+
description:
+

The parameters of the cubic sample (only used if type == cube)

+
+
+
+
cuboid:
+
+
$ref:
+

Cuboid

+
+
description:
+

The parameters of the cuboid sample (only used if type == cuboid)

+
+
+
+
cylinder:
+
+
$ref:
+

Cylinder

+
+
description:
+

The parameters of the cylindrical sample (only used if type == cylinder)

+
+
+
+
margin:
+
+
description:
+

The shape margin used to define how close to the edges particles should be placed (A)

+
+
maxItems:
+

3

+
+
minItems:
+

3

+
+
prefixItems:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    number

    +
    +
    +
    • +
+
+
title:
+

Margin

+
+
type:
+

array

+
+
+
+
+
+
title:
+

Shape

+
+
type:
+

object

+
+
+
+
+

ShapeType

+
+
description:
+

An enumeration of sample shape types

+
+
enum:
+
    +

  • cube

    • +

  • cuboid

    • +

  • cylinder

    • +
+
+
title:
+

ShapeType

+
+
type:
+

string

+
+
+
+
+

Simulation

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe the simulation parameters

+
+
properties:
+
+
slice_thickness:
+
+
description:
+

The multislice thickness (A)

+
+
title:
+

Slice Thickness

+
+
type:
+

number

+
+
+
+
margin:
+
+
description:
+

The margin around the image

+
+
title:
+

Margin

+
+
type:
+

integer

+
+
+
+
padding:
+
+
description:
+

Additional padding

+
+
title:
+

Padding

+
+
type:
+

integer

+
+
+
+
division_thickness:
+
+
description:
+

Deprecated

+
+
title:
+

Division Thickness

+
+
type:
+

integer

+
+
+
+
ice:
+
+
description:
+

Use the Gaussian Random Field ice model (True/False)

+
+
title:
+

Ice

+
+
type:
+

boolean

+
+
+
+
ice_parameters:
+
+
$ref:
+

IceParameters

+
+
description:
+

The parameters for the GRF ice model

+
+
+
+
radiation_damage_model:
+
+
description:
+

Use the radiation damage model (True/False)

+
+
title:
+

Radiation Damage Model

+
+
type:
+

boolean

+
+
+
+
inelastic_model:
+
+
anyOf:
+
+
+
description:
+

The inelastic model parameters

+
+
+
+
mp_loss_width:
+
+
anyOf:
+
    +
  • +
    type:
    +

    number

    +
    +
    +
    • +
  • +
    type:
    +

    null

    +
    +
    +
    • +
+
+
description:
+

The MPL energy filter width

+
+
title:
+

Mp Loss Width

+
+
+
+
mp_loss_position:
+
+
$ref:
+

MPLPosition

+
+
description:
+

The MPL energy filter position

+
+
+
+
sensitivity_coefficient:
+
+
description:
+

The radiation damage model sensitivity coefficient. This value relates the value of an isotropic B factor to the number of incident electrons. Typical values for this (calibrated from X-ray and EM data) range between 0.02 and 0.08 where a higher value will result in a larger B factor.

+
+
title:
+

Sensitivity Coefficient

+
+
type:
+

number

+
+
+
+
+
+
title:
+

Simulation

+
+
type:
+

object

+
+
+
+
+

Sputter

+
+
additionalProperties:
+

False

+
+
description:
+

A model to describe a sputter coating to the sample

+
+
properties:
+
+
element:
+
+
description:
+

The symbol of the atom for the sputter coating material

+
+
title:
+

Element

+
+
type:
+

string

+
+
+
+
thickness:
+
+
description:
+

The thickness of the sputter coating (A)

+
+
title:
+

Thickness

+
+
type:
+

number

+
+
+
+
+
+
required:
+
    +

  • element

    • +

  • thickness

    • +
+
+
title:
+

Sputter

+
+
type:
+

object

+
+
+
+

+

The default configuration parameters can be seen by typing the following +command:

+
+
+

Examples

+
+

Basic configuration

+

This is the default configuration file as output by parakeet.config.new. This configuration file only shows the most useful parameters which you should set.

+
microscope:
+  beam:
+    electrons_per_angstrom: 30
+    energy: 300
+    source_spread: 0.1
+  detector:
+    nx: 1000
+    ny: 1000
+    pixel_size: 1
+  lens:
+    c_10: -20000
+    c_30: 2.7
+    c_c: 2.7
+sample:
+  box:
+  - 1000
+  - 1000
+  - 1000
+  centre:
+  - 500
+  - 500
+  - 500
+  molecules: null
+  shape:
+    cube:
+      length: 1000.0
+    cuboid:
+      length_x: 1000.0
+      length_y: 1000.0
+      length_z: 1000.0
+    cylinder:
+      length: 1000.0
+      radius: 500.0
+    margin:
+    - 0
+    - 0
+    - 0
+    type: cube
+scan:
+  mode: still
+  num_images: 1
+  start_angle: 0
+  step_angle: 0
+simulation:
+  ice: false
+
+
+
+
+

Full configuration

+

The full configuration is somewhat longer and contains parameters which may not +be necessary to modify in most cases:

+
cluster:
+  max_workers: 1
+  method: null
+device: gpu
+microscope:
+  beam:
+    acceleration_voltage_spread: 8.0e-07
+    defocus_drift: null
+    drift: null
+    electrons_per_angstrom: 30
+    energy: 300
+    energy_spread: 2.66e-06
+    phi: 0
+    source_spread: 0.1
+    theta: 0
+  detector:
+    dqe: false
+    nx: 1000
+    ny: 1000
+    origin:
+    - 0
+    - 0
+    pixel_size: 1
+  lens:
+    c_10: -20000
+    c_30: 2.7
+    c_c: 2.7
+    current_spread: 3.3e-07
+  model: null
+  phase_plate: false
+sample:
+  box:
+  - 1000
+  - 1000
+  - 1000
+  centre:
+  - 500
+  - 500
+  - 500
+  ice: null
+  molecules: null
+  shape:
+    cube:
+      length: 1000.0
+    cuboid:
+      length_x: 1000.0
+      length_y: 1000.0
+      length_z: 1000.0
+    cylinder:
+      length: 1000.0
+      radius: 500.0
+    margin:
+    - 0
+    - 0
+    - 0
+    type: cube
+  sputter: null
+scan:
+  axis:
+  - 0
+  - 1
+  - 0
+  exposure_time: 1
+  mode: still
+  num_images: 1
+  start_angle: 0
+  start_pos: 0
+  step_angle: 0
+  step_pos: 0
+simulation:
+  division_thickness: 100
+  ice: false
+  inelastic_model: null
+  margin: 100
+  mp_loss_position: peak
+  mp_loss_width: null
+  padding: 100
+  radiation_damage_model: false
+  sensitivity_coefficient: 0.022
+  slice_thickness: 3.0
+
+
+
+
+

Specifying molecule positions

+

The following snippet will load one locally defined PDB file and will add a +single instance to the sample model. This will put the molecule in the centre +of the sample volume.

+
sample:
+  molecules:
+    local:
+      - filename: myfile.pdb
+        instances: 1
+
+
+

The following snippet will load one locally defined PDB file and will add a 10 +instances to the sample model. This will give the molecules randomly assigned +positions and orientations within the sample volume.

+
sample:
+  molecules:
+    local:
+      - filename: myfile.pdb
+        instances: 10
+
+
+

The following snippet will load two locally defined PDB files and one model +from the PDB. The first model had two instances, the first of which has a +random position and random orientation. The second instance has defined +position and random orientation. The second molecule has two instances, the +first of which has random position and defined orientation and the second +instance has defined position and orientation. The PDB model has 10 instances +with random position and orientation.

+
sample:
+  molecules:
+    local:
+      - filename: myfile.pdb
+        instances:
+          - position: null
+            orientation: null
+          - position: [1, 2, 3]
+            orientation: null
+      - filename: another.pdb
+        instances:
+          - position: null
+            orientation: [1, 2, 3]
+          - position: [1, 2, 3]
+            orientation: [1, 2, 3]
+    pdb:
+      - id: 4V5D
+        instances: 10
+
+
+
+
+

Applying radiation damage

+

Parakeet implements a simple radiation damage model which uses an isotropic B +factor to blur the atomic potential during simulation. The B factor increases +linearly with the incident electron dose according to a sensitivity +coefficient. To apply the beam damage model you can set the following +parameters which will enable the beam damage model and simulate the images +using a dose symmetric scheme.

+
simulation:
+  radiation_damage_model: true
+  sensitivity_coefficient: 0.022
+
+scan:
+  mode: dose_symmetric
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/genindex.html b/docs/genindex.html new file mode 100644 index 00000000..e7df03d9 --- /dev/null +++ b/docs/genindex.html @@ -0,0 +1,435 @@ + + + + + + + + Index — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ _ + | A + | B + | C + | D + | E + | F + | G + | I + | L + | M + | N + | O + | P + | R + | S + | T + +
+

_

+ + +
+ +

A

+ + + +
+ +

B

+ + + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

E

+ + + +
+ +

F

+ + +
+ +

G

+ + + +
+ +

I

+ + + +
+ +

L

+ + + +
+ +

M

+ + + +
+ +

N

+ + + +
+ +

O

+ + + +
+ +

P

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + +
+ + + +
+
+
+ +
+ +
+

© Copyright 2022, James Parkhurst.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 00000000..cf646bf4 --- /dev/null +++ b/docs/index.html @@ -0,0 +1,181 @@ + + + + + + + + + Welcome to parakeet’s documentation! — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Welcome to parakeet’s documentation!

+_images/parakeet_logo.png + +
+

Contents:

+ +
+
+
+

Indices and tables

+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/installation.html b/docs/installation.html new file mode 100644 index 00000000..92ca4def --- /dev/null +++ b/docs/installation.html @@ -0,0 +1,594 @@ + + + + + + + + + Installation — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Installation

+
+

Dependencies

+

In order to build this package, the following dependencies are required:

+
    +

  • A C++ compiler (e.g. g++)

    • +

  • FFTW

    • +

  • Python development libraries

    • +

  • The CUDA toolkit

    • +
+

On ubuntu 20.04, the dependencies can be install on a clean install as follows +(you may need to contact your system administrator if you do not have admin +privileges):

+
# Install GCC
+sudo apt-get install build-essential
+
+# Install FFTW
+sudo apt-get install libfftw3-dev
+
+# Install Python headers
+sudo apt-get install python3.8-dev
+sudo apt-get install python3.8-venv
+
+# Install CUDA toolkit
+wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
+sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
+sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub
+sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
+sudo apt-get update
+sudo apt-get -y install cuda
+
+
+
+
+

Environment variables

+

If you have multiple compiler versions or the compilers you want to use are not +automatically picked up by cmake, you can explicitly state the compiler +versions you would like to use as follows, where in this case we are using gcc +as the C++ compiler:

+
export CXX=/usr/bin/g++
+export CUDACXX=/usr/local/cuda-11/bin/nvcc
+export FFTWDIR=/usr/local/
+
+
+

Depending on your GPU and the version of the CUDA toolkit you are using, it may +also be necessary to set the CMAKE_CUDA_ARCHITECTURES variable. This variable +is by default set to “OFF” in the CMakeLists.txt file which has the effect of +compiling CUDA kernels on the fly. If you have an old GPU, this may not work +and you will receive CUDA errors when attempting to run the simulations on the +GPU. In this case simply set the variable to the architecture supported by your +GPU as follows (the example below is for the compute_37 architecture):

+
export CMAKE_CUDA_ARCHITECTURES=37
+
+
+
+
+

Python virtual environments

+

Before installing parakeet, you may want to setup a python virtual environment +in which to install it rather than installing into your system library. Use the +following commands before following the instructions below.

+
python3 -m venv env
+source env/bin/activate
+
+
+
+
+

Install from source

+

To install from source you can run the following commands after setting the +environment variables described above.

+
# Clone the repository
+git clone https://github.com/rosalindfranklininstitute/parakeet.git
+
+# Enter the parakeet directory
+cd parakeet
+
+# Checkout the submodules
+git submodule update --init --recursive
+
+# Install the package locally
+pip install .
+
+
+
+
+

Installation for developers

+

Run the following commands to install in development mode after setting the +environment variables described above:

+
# Clone the repository
+git clone https://github.com/rosalindfranklininstitute/parakeet.git
+
+# Enter the parakeet directory
+cd parakeet
+
+# Checkout the submodules
+git submodule update --init --recursive
+
+# Install the package locally
+pip install . -e
+
+
+
+
+

Install using PIP

+

You can install parakeet from the python package archive using pip by running +the following command. This is a source package which needs to be built on your +local machine so the environment variables described above for CUDA, FFTW and +CXX may need to be set.

+
pip install python-parakeet
+
+
+

It is also possible to install the version of parakeet on the master branch (or +any other branch) directly using pip by using the following command:

+
python -m pip install git+https://github.com/rosalindfranklininstitute/parakeet.git@master
+
+
+
+
+

Install using conda

+

You can install parakeet using conda as follows:

+
# Create a conda environment
+conda create -n parakeet python=3.9
+
+# Install parakeet
+conda install -c conda-forge -c james.parkhurst python-parakeet
+
+
+
+
+

Install as a Docker container

+

Parakeet can also be run via Docker +(https://www.docker.com/get-started). To pull the docker container with the latest version +parakeet, you can do the following:

+
docker pull quay.io/rosalindfranklininstitute/parakeet:latest
+
+
+

You may also pull the docker container of a specific version of parakeet. To do this in the above +command replace the ‘latest’ with one of the tags that you can find here +( https://quay.io/repository/rosalindfranklininstitute/parakeet?tab=tags).

+

To use parakeet with docker with GPU support the host machine should have the +appropriate Nvidia drivers installed and docker needs to be installed with the +nvidia container toolkit +(https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html).

+

To easily input and output data from the container the volume mechanism can be +used, where a workspace directory of the host machine is mounted to a directory +in the container (in the folder /mnt in the example below). For this reason it +is advised that all the relevant files (e.g. config.yaml, sample.h5, etc.) +should be present in the host workspace directory.

+

Below is an example on how to use parakeet after, its docker image has been pulled, to run parakeet commands:

+
docker run --gpus all -v $(pwd):/mnt --workdir=/mnt parakeet:latest \
+  parakeet.config.new
+
+
+

You may also pull and run parakeet with a single command.

+
docker run --gpus all -v $(pwd):/mnt --workdir=/mnt \
+  quay.io/rosalindfranklininstitute/parakeet:latest parakeet.config.new
+
+
+
+
+

Install as a Singularity image

+

Parakeet can also be run via Singularity +(https://sylabs.io/guides/2.6/user-guide/installation.html). To build +parakeet’s singularity container you can do the following:

+
singularity build parakeet.sif docker://quay.io/rosalindfranklininstitute/parakeet:latest
+
+
+

Again similar to docker, you may build the singularity container of a specific version of parakeet +by replacing the ‘latest’ in the command above with one of the tags that you can find here +( https://quay.io/repository/rosalindfranklininstitute/parakeet?tab=tags).

+

Also like with docker, to use parakeet with singularity and GPU support, the +host machine should have the appropriate Nvidia drivers installed.

+

Below is an example on how to use parakeet, after its singularity image has been build, to run parakeet commands:

+
# You can open an interactive shell in the singularity container like this:
+singularity shell --nv --bind=/data/directory:/mnt --pwd=/mnt parakeet.sif
+
+# Or you can execute multiple commands
+singularity exec --nv --bind=/data/directory:/mnt --pwd=/mnt parakeet.sif \
+  bash -c "parakeet.config.new && parakeet.sample.new"
+
+
+

You may also build and run parakeet with a single command.

+
# You can open an interactive shell in the singularity container like this:
+singularity shell --nv --bind=/data/directory:/mnt --pwd=/mnt \
+  docker://quay.io/rosalindfranklininstitute/parakeet:latest
+
+# Or you can execute multiple commands
+singularity exec --nv --bind=/data/directory:/mnt --pwd=/mnt \
+  docker://quay.io/rosalindfranklininstitute/parakeet:latest \
+  bash -c "parakeet.config.new && parakeet.sample.new"
+
+
+
+
+

Install as Singularity sandbox

+

If you need to modify the singularity container for development purposes, it is +possible to build a parakeet sandbox as follows:

+
singularity build --sandbox parakeet_sandbox/ parakeet.sif
+
+
+

The source code for parakeet resides in the parakeet_sandbox/apps/ directory. +You can then modify the python code in place and use singularity shell or +singularity run to install the changes as follows:

+
singularity run --writable parakeet_sandbox/ pip install /app --prefix=/usr/local
+
+
+

Likewise, new software packages can be install into the container as follows:

+
singularity run --writable parakeet_sandbox/ pip install ${PACKAGE} --prefix=/usr/local
+
+
+

To run parakeet from the sandbox, execute with the following command:

+
singularity run --nv parakeet_sandbox/ parakeet.run -c config.yaml
+
+
+

If you want to rebuild the singularity image from the sandbox you can then do +the following:

+
singularity build parakeet_image.sif parakeet_sandbox/
+
+
+
+
+

Build a derivative Singularity image

+

You can build a new container depending on the parakeet docker container as +follows. In your python source code repository create a file called Dockerfile +with the following contents:

+
FROM quay.io/rosalindfranklininstitute/parakeet:latest
+
+WORKDIR /myapp
+COPY . .
+
+RUN apt update
+RUN git submodule update --init --recursive
+RUN pip install .
+
+
+

Now build locally with docker:

+
sudo docker build . -t me/myapp
+
+
+

Now we can build the singularity image from the docker image

+
singularity build myapp.sif docker-daemon://me/myapp:latest
+
+
+
+
+

Install as a Apptainer image

+

Parakeet can also be run via Apptainer. Apptainer is the new name for the Singularity +project after is official move to the Linux Foundation +(https://apptainer.org/news/community-announcement-20211130/).

+

You may build and run parakeet via an Apptainer container the same way you would +build and run parakeet via an Singularity container, but instead of the command +‘singularity’ the command ‘apptainer’ should be used. The arguments of the command +‘apptainer’ is the exact same with the command ‘singularity’.

+
+
+

Install as a snap

+

You can install the parakeet snap from the snapcraft repository as follows:

+
# Install the snap from the edge channel
+sudo snap install parakeet --classic --edge
+
+
+

You can also build the parakeet snap application from source as follows:

+
# Run this command in the repository directory on a VM with 4GB memory
+SNAPCRAFT_BUILD_ENVIRONMENT_MEMORY=4G snapcraft
+
+# Install the locally built snap
+sudo snap install parakeet_${VERSION}.snap --classic --dangerous
+
+
+

Note that the snap installation only exposes the top level parakeet command:

+
parakeet -h
+
+
+
+
+

Install on Baskerville HPC (native)

+

In order to install parakeet on the Baskerville tier 2 supercomputer (https://www.baskerville.ac.uk/) +within a virtual python environment (https://docs.baskerville.ac.uk/self-install/), +start an interactive job as follows (you will need to know your +account-project code and qos to do this):

+
srun --account=${ACCOUNT} --qos=${QOS} --gpus=1 --time=0:20:0 \
+  --export=USER,HOME,PATH,TERM --pty /bin/bash
+
+
+

When the interactive job starts (you may need to wait until the requested computational resources are +available), execute the following commands to install parakeet:

+
# Load required modules
+module purge
+module load baskerville
+module load CUDA/11.4
+module load FFTW
+module load Python/3
+
+# Create a virtual environment
+python -m venv --system-site-packages env
+source env/bin/activate
+python -m pip install pip --upgrade
+
+# Install parakeet
+python -m pip install python-parakeet
+
+
+

You can run parakeet on Baskerville non-interactively and interactively.

+

To run parakeet on Baskerville non-interactively (https://docs.baskerville.ac.uk/jobs/) +you need write a script called run.sh with the following contents (you will need to know +your account-project code, qos and how much time do you expect to take for your script to finish):

+
#!/bin/bash
+#SBATCH --account=$ACCOUNT
+#SBATCH --qos=$QOS
+#SBATCH --gpus=1
+#SBATCH --time=$TIME
+
+# Load required modules
+module purge
+module load baskerville
+module load CUDA/11.4
+module load FFTW
+module load Python/3
+
+# Activate environment
+source env/bin/activate
+
+# Parakeet commands
+parakeet.run -c config.yaml
+
+
+

To submit the run.sh script and therefore run the parakeet simulations execute the following:

+
sbatch run.sh
+
+
+

The benefit of non-interactive job submissions is that your job will be executed automatically, +when the requested computational resources are available and that you can submit and queue multiple +jobs.

+

To run parakeet interactively (https://docs.baskerville.ac.uk/interactive-jobs/), execute:

+
srun --account=${ACCOUNT} --qos=${QOS} --gpus=1 --time=${TIME} \
+  --export=USER,HOME,PATH,TERM --pty /bin/bash
+
+
+

When the interactive job starts (you may need to wait until the requested computational resources are +available), execute the following commands to install parakeet:

+
# Load required modules
+module purge
+module load baskerville
+module load CUDA/11.4
+module load FFTW
+module load Python/3
+
+# Activate environment
+source env/bin/activate
+
+# Parakeet commands
+parakeet.run -c config.yaml
+
+
+
+
+

Install on Baskerville (apptainer)

+

Alternatively, you may run parakeet on the baskerville tier 2 supercomputer with +apptainer (https://docs.baskerville.ac.uk/containerisation/).

+

To run parakeet on Baskerville non-interactively (https://docs.baskerville.ac.uk/jobs/) +you need write a script called run.sh with the following contents (you will need to know +your account-project code, qos and how much time do you expect to take for your script to finish):

+
#!/bin/bash
+#SBATCH --account=$ACCOUNT
+#SBATCH --qos=$QOS
+#SBATCH --gpus=1
+#SBATCH --time=$TIME
+
+# Load required modules
+module purge
+module load baskerville
+module load CUDA/11.4
+module load FFTW
+module load Python/3
+
+export APPTAINER_CACHEDIR=/path/to/cache/directory/within/your/project/directory
+
+function container {
+  apptainer exec --nv --bind=/path/to/data/directory/within/your/project/directory:/mnt --pwd=/mnt \
+    docker://quay.io/rosalindfranklininstitute/parakeet:latest bash -c "$@"
+}
+
+# Parakeet commands
+container \
+"echo Below you can have multiple commands && \
+parakeet.run -c config.yaml"
+
+
+

To submit the run.sh script and therefore run the parakeet simulations execute the following:

+
sbatch run.sh
+
+
+

The benefit of non-interactive job submissions is that your job will be executed automatically, +when the requested computational resources are available and that you can submit and queue multiple +jobs.

+

To run parakeet interactively (https://docs.baskerville.ac.uk/interactive-jobs/), execute:

+
srun --account=${ACCOUNT} --qos=${QOS} --gpus=1 --time=${TIME} \
+  --export=USER,HOME,PATH,TERM --pty /bin/bash
+
+
+

When the interactive job starts (you may need to wait until the requested computational resources are +available), execute the following commands to install parakeet:

+
# Load required modules
+module purge
+module load baskerville
+module load CUDA/11.4
+module load FFTW
+module load Python/3
+
+export APPTAINER_CACHEDIR=/path/to/cache/directory/within/your/project/directory
+
+function container {
+  apptainer exec --nv --bind=/path/to/data/directory/within/your/project/directory:/mnt --pwd=/mnt \
+    docker://quay.io/rosalindfranklininstitute/parakeet:latest bash -c "$@"
+}
+
+# Parakeet commands
+container \
+"echo Below you can have multiple commands && \
+parakeet.run -c config.yaml"
+
+
+
+
+

Install on STFC Scarf

+

In order to install parakeet on the scarf with singularity, start and +interactive job as follows:

+
salloc --time=1:0:0
+
+
+

Now run the following commands:

+
singularity build parakeet.sif docker://quay.io/rosalindfranklininstitute/parakeet:latest
+
+
+

Once you are happy, log out of the interactive node. To run parakeet on scarf +write a script called run.sh with the following contents:

+
#!/bin/bash
+#SBATCH --gpus=1
+
+function container {
+  singularity exec --nv --bind=/path/to/data/directory/within/your/project/directory:/mnt --pwd=/mnt \
+    docker://quay.io/rosalindfranklininstitute/parakeet:latest bash -c "$@"
+}
+
+# Parakeet commands
+container \
+"echo Below you can have multiple commands && \
+parakeet.run -c config.yaml"
+
+
+

Then run the simulations as follows:

+
sbatch run.sh
+
+
+
+
+

Testing

+

To run the tests, follow the Installation for developers instructions +and then do the following command from within the source distribution:

+
pytest
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/objects.inv b/docs/objects.inv new file mode 100644 index 00000000..aa78b290 Binary files /dev/null and b/docs/objects.inv differ diff --git a/docs/publications.html b/docs/publications.html new file mode 100644 index 00000000..85e72779 --- /dev/null +++ b/docs/publications.html @@ -0,0 +1,120 @@ + + + + + + + + + Publications — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Publications

+

If you find parakeet useful for you work, please consider citing our paper:

+
+

Parkhurst, J. M., Dumoux, M., Basham, M., Clare, D., Siebert, C. A., Varslot, +T., Kirkland, A., Naismith, J. H., & Evans, G. (2021). Parakeet: A digital +twin software pipeline to assess the impact of experimental parameters on +tomographic reconstructions for cryo-electron tomography. Open Biology, +11(10). https://doi.org/10.1098/rsob.210160

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/search.html b/docs/search.html new file mode 100644 index 00000000..23d39ef1 --- /dev/null +++ b/docs/search.html @@ -0,0 +1,125 @@ + + + + + + + + Search — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+
+ +
+ +
+

© Copyright 2022, James Parkhurst.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/docs/searchindex.js b/docs/searchindex.js new file mode 100644 index 00000000..c4db7678 --- /dev/null +++ b/docs/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Analysis functions": [[0, "analysis-functions"], [5, "analysis-functions"]], "Analysis programs": [[6, "analysis-programs"]], "Applying radiation damage": [[1, "applying-radiation-damage"]], "Auto": [[1, "auto"]], "Basic configuration": [[1, "basic-configuration"]], "Beam": [[1, "beam"]], "Build a derivative Singularity image": [[3, "build-a-derivative-singularity-image"]], "Command line programs": [[6, null]], "Config file manipulation programs": [[6, "config-file-manipulation-programs"]], "Configuration": [[1, null]], "Configuration functions": [[0, "configuration-functions"]], "Contents:": [[2, null]], "CoordinateFile": [[1, "coordinatefile"]], "Cube": [[1, "cube"]], "Cuboid": [[1, "cuboid"]], "Cylinder": [[1, "cylinder"]], "Data models": [[0, "data-models"]], "Definitions": [[1, "definitions"]], "Dependencies": [[3, "dependencies"]], "Detector": [[1, "detector"]], "Device": [[1, "device"]], "Drift": [[1, "drift"]], "Edit the configuration file": [[5, "edit-the-configuration-file"]], "Environment variables": [[3, "environment-variables"]], "Examples": [[1, "examples"]], "Export functions": [[5, "export-functions"]], "Full configuration": [[1, "full-configuration"]], "Generate a new configuration file": [[5, "generate-a-new-configuration-file"]], "Generate sample model": [[5, "generate-sample-model"]], "Ice": [[1, "ice"]], "IceParameters": [[1, "iceparameters"]], "Image IO functions": [[0, "image-io-functions"]], "Image Simulation programs": [[6, "image-simulation-programs"]], "Image simulation functions": [[0, "image-simulation-functions"]], "Indices and tables": [[2, "indices-and-tables"]], "InelasticModel": [[1, "inelasticmodel"]], "Install as Singularity sandbox": [[3, "install-as-singularity-sandbox"]], "Install as a Apptainer image": [[3, "install-as-a-apptainer-image"]], "Install as a Docker container": [[3, "install-as-a-docker-container"]], "Install as a Singularity image": [[3, "install-as-a-singularity-image"]], "Install as a snap": [[3, "install-as-a-snap"]], "Install from source": [[3, "install-from-source"]], "Install on Baskerville (apptainer)": [[3, "install-on-baskerville-apptainer"]], "Install on Baskerville HPC (native)": [[3, "install-on-baskerville-hpc-native"]], "Install on STFC Scarf": [[3, "install-on-stfc-scarf"]], "Install using PIP": [[3, "install-using-pip"]], "Install using conda": [[3, "install-using-conda"]], "Installation": [[3, null]], "Installation for developers": [[3, "installation-for-developers"]], "Lens": [[1, "lens"]], "LocalMolecule": [[1, "localmolecule"]], "MPLPosition": [[1, "mplposition"]], "Microscope": [[1, "microscope"]], "MicroscopeModel": [[1, "microscopemodel"]], "MoleculePose": [[1, "moleculepose"]], "Molecules": [[1, "molecules"]], "Multiprocessing": [[1, "multiprocessing"]], "Named Arguments": [[6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments"], [6, "named-arguments_repeat1"], [6, "named-arguments_repeat2"], [6, "named-arguments_repeat3"], [6, "named-arguments_repeat4"], [6, "named-arguments_repeat5"], [6, "named-arguments_repeat6"], [6, "named-arguments_repeat7"], [6, "named-arguments_repeat8"], [6, "named-arguments_repeat9"], [6, "named-arguments_repeat10"], [6, "named-arguments_repeat11"], [6, "named-arguments_repeat12"], [6, "named-arguments_repeat13"], [6, "named-arguments_repeat14"], [6, "named-arguments_repeat15"], [6, "named-arguments_repeat16"], [6, "named-arguments_repeat17"], [6, "named-arguments_repeat18"], [6, "named-arguments_repeat19"], [6, "named-arguments_repeat20"], [6, "named-arguments_repeat21"], [6, "named-arguments_repeat22"]], "Other programs": [[6, "other-programs"]], "PDB file functions": [[0, "pdb-file-functions"]], "PDB file programs": [[6, "pdb-file-programs"]], "PDBMolecule": [[1, "pdbmolecule"]], "PhasePlate": [[1, "phaseplate"]], "Positional Arguments": [[6, "positional-arguments"], [6, "positional-arguments"], [6, "positional-arguments"], [6, "positional-arguments"], [6, "positional-arguments"], [6, "positional-arguments_repeat1"], [6, "positional-arguments_repeat2"], [6, "positional-arguments_repeat3"], [6, "positional-arguments_repeat4"], [6, "positional-arguments_repeat5"], [6, "positional-arguments_repeat6"], [6, "positional-arguments_repeat7"], [6, "positional-arguments_repeat8"], [6, "positional-arguments_repeat9"]], "Publications": [[4, null]], "Python API": [[0, null]], "Python virtual environments": [[3, "python-virtual-environments"]], "Sample": [[1, "sample"]], "Sample functions": [[0, "sample-functions"]], "Sample manipulation programs": [[6, "sample-manipulation-programs"]], "SampleMotion": [[1, "samplemotion"]], "Scan": [[1, "scan"]], "ScanMode": [[1, "scanmode"]], "Shape": [[1, "shape"]], "ShapeType": [[1, "shapetype"]], "Simulate EM images": [[5, "simulate-em-images"]], "Simulation": [[1, "simulation"]], "Specifying molecule positions": [[1, "specifying-molecule-positions"]], "Sputter": [[1, "sputter"]], "Sub-commands": [[6, "Sub-commands"], [6, "Sub-commands_repeat1"], [6, "Sub-commands_repeat2"], [6, "Sub-commands_repeat3"], [6, "Sub-commands_repeat4"], [6, "Sub-commands_repeat5"], [6, "Sub-commands_repeat6"]], "Testing": [[3, "testing"]], "Tutorial": [[5, null]], "Welcome to 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(parakeet.beam.beam method)": [[0, "parakeet.beam.Beam.__init__", false]], "__init__() (parakeet.detector.detector method)": [[0, "parakeet.detector.Detector.__init__", false]], "__init__() (parakeet.lens.lens method)": [[0, "parakeet.lens.Lens.__init__", false]], "__init__() (parakeet.microscope.microscope method)": [[0, "parakeet.microscope.Microscope.__init__", false]], "__init__() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.__init__", false]], "__init__() (parakeet.scan.scan method)": [[0, "parakeet.scan.Scan.__init__", false]], "acceleration_voltage_spread (parakeet.beam.beam property)": [[0, "parakeet.beam.Beam.acceleration_voltage_spread", false]], "add_atoms() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.add_atoms", false]], "add_molecule() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.add_molecule", false]], "add_molecules() (in module parakeet.sample)": [[0, "parakeet.sample.add_molecules", false]], "angles 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"beam_tilt_theta (parakeet.scan.scan property)": [[0, "parakeet.scan.Scan.beam_tilt_theta", false]], "bounding_box (parakeet.sample.sample property)": [[0, "parakeet.sample.Sample.bounding_box", false]], "centre (parakeet.sample.sample property)": [[0, "parakeet.sample.Sample.centre", false]], "close() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.close", false]], "containing_box (parakeet.sample.sample property)": [[0, "parakeet.sample.Sample.containing_box", false]], "correct() (in module parakeet.analyse)": [[0, "parakeet.analyse.correct", false]], "ctf() (in module parakeet.simulate)": [[0, "parakeet.simulate.ctf", false]], "defocus_offset (parakeet.scan.scan property)": [[0, "parakeet.scan.Scan.defocus_offset", false]], "del_atoms() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.del_atoms", false]], "detector (class in parakeet.detector)": [[0, "parakeet.detector.Detector", false]], "detector (parakeet.microscope.microscope property)": [[0, "parakeet.microscope.Microscope.detector", false]], "dimensions (parakeet.sample.sample property)": [[0, "parakeet.sample.Sample.dimensions", false]], "electrons_per_angstrom (parakeet.beam.beam property)": [[0, "parakeet.beam.Beam.electrons_per_angstrom", false]], "electrons_per_angstrom (parakeet.scan.scan property)": [[0, "parakeet.scan.Scan.electrons_per_angstrom", false]], "energy (parakeet.beam.beam property)": [[0, "parakeet.beam.Beam.energy", false]], "energy_spread (parakeet.beam.beam property)": [[0, "parakeet.beam.Beam.energy_spread", false]], "euler_angles (parakeet.scan.scan property)": [[0, "parakeet.scan.Scan.euler_angles", false]], "exit_wave() (in module parakeet.simulate)": [[0, "parakeet.simulate.exit_wave", false]], "exposure_time (parakeet.scan.scan property)": [[0, "parakeet.scan.Scan.exposure_time", false]], "extract() (in module parakeet.analyse)": [[0, "parakeet.analyse.extract", false]], "fraction_number (parakeet.scan.scan property)": [[0, "parakeet.scan.Scan.fraction_number", false]], "get_atoms() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.get_atoms", false]], "get_atoms_in_fov() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.get_atoms_in_fov", false]], "get_atoms_in_group() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.get_atoms_in_group", false]], "get_atoms_in_range() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.get_atoms_in_range", false]], "get_molecule() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.get_molecule", false]], "get_pdb() (in module parakeet.data)": [[0, "parakeet.data.get_pdb", false]], "identifier() (parakeet.sample.sample method)": [[0, "parakeet.sample.Sample.identifier", false]], "illumination_semiangle (parakeet.beam.beam property)": [[0, "parakeet.beam.Beam.illumination_semiangle", false]], "image() (in module parakeet.simulate)": [[0, "parakeet.simulate.image", false]], "image_number (parakeet.scan.scan 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2, 4, 5, 6], "usag": 6, "user": 3, "usr": 3, "usual": 1, "v": [0, 1, 3], "valu": [0, 1, 6], "variabl": 2, "varslot": 4, "vector": 1, "veloc": 1, "venv": 3, "version": 3, "via": [1, 3], "view": 0, "virtual": 2, "viscek": 1, "vm": 3, "vmax": [0, 6], "vmin": [0, 6], "voltag": 1, "volum": [0, 1, 3, 5, 6], "vortex": 0, "wai": [3, 5], "wait": 3, "want": [0, 3], "water": 1, "wave": [0, 1, 5, 6], "we": [0, 3, 5], "wget": 3, "when": [1, 3, 6], "where": [0, 1, 3], "whether": 1, "which": [0, 1, 3, 5, 6], "whole": 6, "width": [0, 1], "within": [0, 1, 3, 5], "work": [3, 4], "workdir": 3, "workspac": 3, "would": 3, "writabl": 3, "write": [0, 3], "writer": 0, "written": 6, "www": 3, "x": [0, 1], "x0": [0, 6], "x1": [0, 6], "x86_64": 3, "xmipp": 0, "y": [0, 1, 3], "y0": 6, "y1": 6, "yaml": [0, 1, 3, 5, 6], "yet": 5, "yield": 0, "you": [1, 3, 4], "your": 3, "z": [0, 1], "zero": 1, "zero_loss": 1, "zyz": 0}, "titles": ["Python API", "Configuration", "Welcome to parakeet\u2019s documentation!", "Installation", "Publications", "Tutorial", "Command line programs"], "titleterms": {"": 2, "add_molecul": 6, "analys": 6, "analysi": [0, 5, 6], "api": 0, "appli": 1, "apptain": 3, "argument": 6, "auto": 1, "average_all_particl": 6, "average_particl": 6, "basic": 1, "baskervil": 3, "beam": 1, "build": 3, "command": 6, "conda": 3, "config": 6, "configur": [0, 1, 5], "contain": 3, "content": 2, "coordinatefil": 1, "correct": 6, "ctf": 6, "cube": 1, "cuboid": 1, "cylind": 1, "damag": 1, "data": 0, "definit": 1, "depend": 3, "deriv": 3, "detector": 1, "develop": 3, "devic": 1, "docker": 3, "document": 2, "drift": 1, "edit": [5, 6], "em": 5, "environ": 3, "exampl": 1, "exit_wav": 6, "export": [5, 6], "extract": 6, "file": [0, 5, 6], "from": 3, "full": 1, "function": [0, 5], "gener": 5, "get": 6, "hpc": 3, "ic": 1, "iceparamet": 1, "imag": [0, 3, 5, 6], "indic": 2, "inelasticmodel": 1, "instal": 3, "io": 0, "len": 1, "line": 6, "localmolecul": 1, "manipul": 6, "metadata": 6, "microscop": 1, "microscopemodel": 1, "mill": 6, "model": [0, 5], "molecul": 1, "moleculepos": 1, "mplposit": 1, "multiprocess": 1, "name": 6, "nativ": 3, "new": [5, 6], "optic": 6, "other": 6, "parakeet": [2, 6], "pdb": [0, 6], "pdbmolecul": 1, "phasepl": 1, "pip": 3, "posit": [1, 6], "potenti": 6, "program": 6, "public": 4, "python": [0, 3], "radiat": 1, "read": 6, "reconstruct": 6, "refin": 6, "run": 6, "sampl": [0, 1, 5, 6], "samplemot": 1, "sandbox": 3, "scan": 1, "scanmod": 1, "scarf": 3, "shape": 1, "shapetyp": 1, "show": 6, "simpl": 6, "simul": [0, 1, 5, 6], "singular": 3, "snap": 3, "sourc": 3, "specifi": 1, "sputter": [1, 6], "stfc": 3, "sub": 6, "tabl": 2, "test": 3, "tutori": 5, "us": 3, "variabl": 3, "virtual": 3, "welcom": 2}}) \ No newline at end of file diff --git a/docs/tutorial.html b/docs/tutorial.html new file mode 100644 index 00000000..60e05342 --- /dev/null +++ b/docs/tutorial.html @@ -0,0 +1,306 @@ + + + + + + + + + Tutorial — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Tutorial

+

Simulation of datasets is split into a number of different commands. Each +command takes a set of command line options or a configuration file in YAML +format.

+
+

Generate a new configuration file

+
parakeet.config.new
+
+
+

This will generate a new file called config.yaml which will contain the +following configuration.

+
microscope:
+  beam:
+    electrons_per_angstrom: 30
+    energy: 300
+    source_spread: 0.1
+  detector:
+    nx: 1000
+    ny: 1000
+    pixel_size: 1
+  lens:
+    c_10: -20000
+    c_30: 2.7
+    c_c: 2.7
+sample:
+  box:
+  - 1000
+  - 1000
+  - 1000
+  centre:
+  - 500
+  - 500
+  - 500
+  molecules: null
+  shape:
+    cube:
+      length: 1000.0
+    cuboid:
+      length_x: 1000.0
+      length_y: 1000.0
+      length_z: 1000.0
+    cylinder:
+      length: 1000.0
+      radius: 500.0
+    margin:
+    - 0
+    - 0
+    - 0
+    type: cube
+scan:
+  mode: still
+  num_images: 1
+  start_angle: 0
+  step_angle: 0
+simulation:
+  ice: false
+
+
+
+
+

Edit the configuration file

+

The configuration file now needs to be edited to perform the desired +simulation. For example, to simulate with a single molecule we modify the +sample.molecules field as follows.

+
microscope:
+  beam:
+    electrons_per_angstrom: 30
+    energy: 300
+    source_spread: 0.1
+  detector:
+    nx: 1000
+    ny: 1000
+    pixel_size: 1
+  lens:
+    c_10: -20000
+    c_30: 2.7
+    c_c: 2.7
+sample:
+  box:
+  - 1000
+  - 1000
+  - 1000
+  centre:
+  - 500
+  - 500
+  - 500
+  molecules:
+    pdb:
+      - id: 4v1w
+        instances: 1
+  shape:
+    cube:
+      length: 1000.0
+    cuboid:
+      length_x: 1000.0
+      length_y: 1000.0
+      length_z: 1000.0
+    cylinder:
+      length: 1000.0
+      radius: 500.0
+    margin:
+    - 0
+    - 0
+    - 0
+    type: cube
+scan:
+  mode: still
+  num_images: 1
+  start_angle: 0
+  step_angle: 0
+simulation:
+  ice: false
+
+
+
+
+

Generate sample model

+

Once the configuration file has been generated a new sample file can be created +with the following command:

+
parakeet.sample.new -c config.yaml
+
+
+

This will result in a file “sample.h5” being generated. This file contains +information about the size and shape of the sample but as yet doesn’t contain +any atomic coordinates. The atomic model is added by running the following +command which adds molecules to the sample file. If a single molcule is +specified then it will be placed in the centre of the sample volume. If +multiple molecules are specified then the molecules will be positioned at +random locations in the sample volume. This command will update the “sample.h5” +file with the atomic coordinates but will not generated any new files.

+
parakeet.sample.add_molecules -c config.yaml
+
+
+
+
+

Simulate EM images

+

Once the atomic model is ready, the EM images can be simulated with the +following commands. Each stage of the simulation is separated because it may be +desirable to simulate many different defocused images from the sample exit wave +for example or many different doses for the sample defocusses image. Being +separate, the output of one stage can be reused for multiple runs of the next +stage. The first stage is to simulate the exit wave. This is the propagation of +the electron wave through the sample. It is therefore the most computationally +intensive part of the processes since the contribution of all atoms within the +sample needs to be calculated.

+
parakeet.simulate.exit_wave -c config.yaml
+
+
+

This command will generate a file “exit_wave.h5” which will contain the exit +wave of all tilt angles. The next step is to simulate the micropscope optics +which is done with the following command:

+
parakeet.simulate.optics -c config.yaml
+
+
+

This step is much quicker as it only scales with the size of the detector image +and doesn’t require the atomic coordinates again. The command will output a +file “optics.h5”. Finally, the response of the detector can be simulated with +the following command:

+
parakeet.simulate.image -c config.yaml
+
+
+

This command will add the detector DQE and the Poisson noise for a given dose +and will output a file “image.h5”.

+
+
+

Export functions

+

Typically we cant to output an MRC file for further processing. The hdf5 files +can easily be exported to MRC by the following command:

+
parakeet.export file.h5 -o file.mrc
+
+
+

The export command can also be used to rebin the image or select a region of interest.

+
+
+

Analysis functions

+

The reconstruction function can be called in Parakeet in the following way:

+
parakeet.export image.h5 -o image.mrc
+parakeet.analyse.reconstruct -c config.yaml -i image.mrc
+
+
+

Averaging of the particles can then be done with:

+
parakeet.analyse.average_particles -c config.yaml
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/usage.html b/docs/usage.html new file mode 100644 index 00000000..14d8b3b5 --- /dev/null +++ b/docs/usage.html @@ -0,0 +1,1792 @@ + + + + + + + + + Command line programs — parakeet 0.1.dev1+gfc2137f documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Command line programs

+
+

Config file manipulation programs

+
+

parakeet.config.new

+

Generate a new config file

+

+
usage: parakeet.config.new [-h] [-c CONFIG] [-f FULL]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+

Default: “config.yaml”

+
+
-f, --full
+

Generate a file with the full configuration specification

+

Default: False

+
+
+
+
+
+

parakeet.config.show

+

Show the configuration

+

+
usage: parakeet.config.show [-h] [-c CONFIG] [-s SCHEMA]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --schema
+

Show the config schema. +To show full scheme type ‘-s .’. +To show the schema for a specific section type e.g. ‘-s /definitions/Simulation’

+
+
+
+
+
+

parakeet.config.edit

+

Edit the configuration

+

+
usage: parakeet.config.edit [-h] -i INPUT -o OUTPUT -s CONFIG
+
+
+
+

Named Arguments

+
+
-i, --input
+

The input yaml file to configure the simulation

+
+
-o, --output
+

The output yaml file to configure the simulation

+
+
-s
+

The configuration string

+

Default: “”

+
+
+
+
+
+
+

Sample manipulation programs

+
+

parakeet.sample.new

+

Create a new sample model

+

+
usage: parakeet.sample.new [-h] -c CONFIG [-s SAMPLE]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+

parakeet.sample.add_molecules

+

Add molecules to the sample model

+

+
usage: parakeet.sample.add_molecules [-h] -c CONFIG [-s SAMPLE]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+

parakeet.sample.mill

+

Mill the sample

+

+
usage: parakeet.sample.mill [-h] -c CONFIG [-s SAMPLE]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+

parakeet.sample.sputter

+

Sputter the sample

+

+
usage: parakeet.sample.sputter [-h] -c CONFIG [-s SAMPLE]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+

parakeet.sample.show

+

Print details about the sample model

+

+
usage: parakeet.sample.show [-h] [-s SAMPLE]
+
+
+
+

Named Arguments

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+
+

Image Simulation programs

+
+

parakeet.simulate.potential

+

Simulate the projected potential from the sample

+

+
usage: parakeet.simulate.potential [-h] -c CONFIG [-s SAMPLE] [-p POTENTIAL]
+                                   [-d {cpu,gpu}] [--nproc NPROC]
+                                   [--gpu_id GPU_ID]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-p, --potential
+

The prefix for the filename for the potential

+

Default: “potential”

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
+
+
+
+

parakeet.simulate.exit_wave

+

Simulate the exit wave from the sample

+

+
usage: parakeet.simulate.exit_wave [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE]
+                                   [-d {cpu,gpu}] [--nproc NPROC]
+                                   [--gpu_id GPU_ID]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-e, --exit_wave
+

The filename for the exit wave

+

Default: “exit_wave.h5”

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
+
+
+
+

parakeet.simulate.optics

+

Simulate the optics and infinite dose image

+

+
usage: parakeet.simulate.optics [-h] -c CONFIG [-d {cpu,gpu}] [--nproc NPROC]
+                                [--gpu_id GPU_ID] [-e EXIT_WAVE] [-o OPTICS]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
-e, --exit_wave
+

The filename for the exit wave

+

Default: “exit_wave.h5”

+
+
-o, --optics
+

The filename for the optics

+

Default: “optics.h5”

+
+
+
+
+
+

parakeet.simulate.ctf

+

Simulate the ctf

+

+
usage: parakeet.simulate.ctf [-h] -c CONFIG [-o OUTPUT]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-o
+

The filename for the output

+

Default: “ctf.h5”

+
+
+
+
+
+

parakeet.simulate.image

+

Simulate the noisy detector image

+

+
usage: parakeet.simulate.image [-h] -c CONFIG [-o OPTICS] [-i IMAGE]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-o, --optics
+

The filename for the optics

+

Default: “optics.h5”

+
+
-i, --image
+

The filename for the image

+

Default: “image.h5”

+
+
+
+
+
+

parakeet.simulate.simple

+

Simulate the whole process

+

+
usage: parakeet.simulate.simple [-h] -c CONFIG [-o OUTPUT] [atoms]
+
+
+
+

Positional Arguments

+
+
atoms
+

The filename for the input atoms

+
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-o, --output
+

The filename for the output

+

Default: “output.h5”

+
+
+
+
+
+
+

Analysis programs

+
+

parakeet.analyse.reconstruct

+

Reconstruct the volume

+

+
usage: parakeet.analyse.reconstruct [-h] -c CONFIG [-d {cpu,gpu}] [-i IMAGE]
+                                    [-r REC]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
-i, --image
+

The filename for the image

+

Default: “image.mrc”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
+
+
+
+

parakeet.analyse.correct

+

3D CTF correction of the images

+

+
usage: parakeet.analyse.correct [-h] -c CONFIG [-i IMAGE] [-cr CORRECTED]
+                                [-ndf NUM_DEFOCUS] [-d {cpu,gpu}]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-i, --image
+

The filename for the image

+

Default: “image.mrc”

+
+
-cr, --corrected
+

The filename for the corrected image

+

Default: “corrected_image.mrc”

+
+
-ndf, --num-defocus
+

Number of defoci that correspond to different depths through for which the sample will be 3D CTF corrected

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
+
+
+
+

parakeet.analyse.average_particles

+

Perform sub tomogram averaging

+

+
usage: parakeet.analyse.average_particles [-h] -c CONFIG [-s SAMPLE] [-r REC]
+                                          [-h1 HALF1] [-h2 HALF2]
+                                          [-psz PARTICLE_SIZE]
+                                          [-n NUM_PARTICLES]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
-h1, --half1
+

The filename for the particle average

+

Default: “half1.mrc”

+
+
-h2, --half2
+

The filename for the particle average

+

Default: “half2.mrc”

+
+
-psz, --particle_size
+

The size of the particles extracted (px)

+

Default: 0

+
+
-n, --num_particles
+

The number of particles to use

+

Default: 0

+
+
+
+
+
+

parakeet.analyse.average_all_particles

+

Perform sub tomogram averaging

+

+
usage: parakeet.analyse.average_all_particles [-h] -c CONFIG [-s SAMPLE]
+                                              [-r REC] [-avm AVERAGE]
+                                              [-psz PARTICLE_SIZE]
+                                              [-n NUM_PARTICLES]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
-avm, --average_map
+

The filename for the particle average

+

Default: “average_map.mrc”

+
+
-psz, --particle_size
+

The size of the particles extracted (px)

+

Default: 0

+
+
-n, --num_particles
+

The number of particles to use

+

Default: 0

+
+
+
+
+
+

parakeet.analyse.extract

+

Perform sub tomogram extraction

+

+
usage: parakeet.analyse.extract [-h] -c CONFIG [-s SAMPLE] [-r REC]
+                                [-pm PARTICLES] [-psz PARTICLE_SIZE]
+                                [-psm PARTICLE_SAMPLING]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
-pm, --particle_map
+

The filename for the particle average

+

Default: “particle_map.h5”

+
+
-psz, --particle_size
+

The size of the particles extracted (px)

+

Default: 0

+
+
-psm, --particle_sampling
+

The sampling of the particle volume (factor of 2)

+

Default: 1

+
+
+
+
+
+

parakeet.analyse.refine

+

Refine map and model

+

+
usage: parakeet.analyse.refine [-h] -c CONFIG [-s SAMPLE] [-r REC]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “half1.mrc”

+
+
+
+
+
+
+

PDB file programs

+
+

parakeet.pdb.read

+

Read a PDB file

+

+
usage: parakeet.pdb.read [-h] filename
+
+
+
+

Positional Arguments

+
+
filename
+

The path to the PDB file

+
+
+
+
+
+

parakeet.pdb.get

+

Get a PDB file

+

+
usage: parakeet.pdb.get [-h] [-d DIRECTORY] id
+
+
+
+

Positional Arguments

+
+
id
+

The PDB ID

+
+
+
+
+

Named Arguments

+
+
-d, --directory
+

The directory to save to

+

Default: “.”

+
+
+
+
+
+
+

Other programs

+
+

parakeet.export

+

Export images to a different format

+

+
usage: parakeet.export [-h] -o OUTPUT [--rot90 ROT90]
+                       [--rotation_range ROTATION_RANGE | --select_images SELECT_IMAGES]
+                       [--roi ROI]
+                       [--complex_mode {complex,real,imaginary,amplitude,phase,phase_unwrap,square,imaginary_square}]
+                       [--interlace INTERLACE] [--rebin REBIN]
+                       [--filter_resolution FILTER_RESOLUTION]
+                       [--filter_shape {square,gaussian}] [--vmin VMIN]
+                       [--vmax VMAX] [--sort {angle}]
+                       filename
+
+
+
+

Positional Arguments

+
+
filename
+

The input filename

+
+
+
+
+

Named Arguments

+
+
-o, --output
+

The output filename

+
+
--rot90
+

Rotate the image 90deg counter clockwise

+

Default: False

+
+
--rotation_range
+

Select a rotation range (deg).

+

Multiple rotation ranges can be specified as: +–rotation_range=start1,stop1;start2,stop2

+
+
--select_images
+

Select a range of images (start,stop,step)

+
+
--roi
+

Select a region of interest (–roi=x0,y0,x1,y1)

+
+
--complex_mode
+

Possible choices: complex, real, imaginary, amplitude, phase, phase_unwrap, square, imaginary_square

+

How to treat complex numbers

+

Default: “complex”

+
+
--interlace
+

Interlace the scan. If the value <= 1 then the images are kept in the same order, otherwise, the images are reordered by skipping images. For example, if –interlace=2 is set then the images will be written out as [1, 3, 5, … , 2, 4, 6, …]

+
+
--rebin
+

The rebinned factor. The shape of the output images will be original_shape / rebin

+

Default: 1

+
+
--filter_resolution
+

The resolution of the filter (A)

+
+
--filter_shape
+

Possible choices: square, gaussian

+

The shape of the filter

+
+
--vmin
+

The minimum pixel value when exporting to an image

+
+
--vmax
+

The maximum pixel value when exporting to an image

+
+
--sort
+

Possible choices: angle

+

Sort the images

+
+
+
+
+
+

parakeet.run

+

Run full simulation experiment

+

+
usage: parakeet.run [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE] [-o OPTICS]
+                    [-i IMAGE] [-d {cpu,gpu}] [--nproc NPROC]
+                    [--gpu_id GPU_ID]
+                    [--steps {all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} [{all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} ...]]
+
+
+
+

Named Arguments

+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-e, --exit_wave
+

The filename for the exit wave

+

Default: “exit_wave.h5”

+
+
-o, --optics
+

The filename for the optics

+

Default: “optics.h5”

+
+
-i, --image
+

The filename for the image

+

Default: “image.h5”

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
--steps
+

Possible choices: all, sample, sample.new, sample.add_molecules, simulate, simulate.exit_wave, simulate.optics, simulate.image

+

Which simulation steps to run

+
+
+
+
+
+

parakeet

+

Parakeet: simulate some TEM images!

+

+
usage: parakeet [-h]
+                {config,sample,simulate,analyse,metadata,pdb,export,run} ...
+
+
+
+

Positional Arguments

+
+
command
+

Possible choices: config, sample, simulate, analyse, metadata, pdb, export, run

+

The parakeet sub commands

+
+
+
+
+

Sub-commands

+
+
config
+

Commands to manipulate configuration files

+
parakeet config [-h] {new,edit,show} ...
+
+
+
+
Positional Arguments
+
+
config_command
+

Possible choices: new, edit, show

+

The parakeet config sub commands

+
+
+
+
+
Sub-commands
+
+
new
+

Generate a new config file

+
parakeet config new [-h] [-c CONFIG] [-f FULL]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+

Default: “config.yaml”

+
+
-f, --full
+

Generate a file with the full configuration specification

+

Default: False

+
+
+
+
+
+
edit
+

Edit the configuration

+
parakeet config edit [-h] -i INPUT -o OUTPUT -s CONFIG
+
+
+
+
Named Arguments
+
+
-i, --input
+

The input yaml file to configure the simulation

+
+
-o, --output
+

The output yaml file to configure the simulation

+
+
-s
+

The configuration string

+

Default: “”

+
+
+
+
+
+
show
+

Show the configuration

+
parakeet config show [-h] [-c CONFIG] [-s SCHEMA]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --schema
+

Show the config schema. +To show full scheme type ‘-s .’. +To show the schema for a specific section type e.g. ‘-s /definitions/Simulation’

+
+
+
+
+
+
+
+
sample
+

Commands to manipulate the sample files

+
parakeet sample [-h] {new,add_molecules,mill,sputter,show} ...
+
+
+
+
Positional Arguments
+
+
sample_command
+

Possible choices: new, add_molecules, mill, sputter, show

+

The parakeet sample sub commands

+
+
+
+
+
Sub-commands
+
+
new
+

Create a new sample model

+
parakeet sample new [-h] -c CONFIG [-s SAMPLE]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+
add_molecules
+

Add molecules to the sample model

+
parakeet sample add_molecules [-h] -c CONFIG [-s SAMPLE]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+
mill
+

Mill the sample

+
parakeet sample mill [-h] -c CONFIG [-s SAMPLE]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+
sputter
+

Sputter the sample

+
parakeet sample sputter [-h] -c CONFIG [-s SAMPLE]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+
show
+

Print details about the sample model

+
parakeet sample show [-h] [-s SAMPLE]
+
+
+
+
Named Arguments
+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
+
+
+
+
+
+
simulate
+

Commands to simulate the TEM images

+
parakeet simulate [-h] {potential,exit_wave,optics,image,ctf} ...
+
+
+
+
Positional Arguments
+
+
simulate_command
+

Possible choices: potential, exit_wave, optics, image, ctf

+

The parakeet simulate sub commands

+
+
+
+
+
Sub-commands
+
+
potential
+

Simulate the projected potential from the sample

+
parakeet simulate potential [-h] -c CONFIG [-s SAMPLE] [-p POTENTIAL]
+                            [-d {cpu,gpu}] [--nproc NPROC] [--gpu_id GPU_ID]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-p, --potential
+

The prefix for the filename for the potential

+

Default: “potential”

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
+
+
+
+
exit_wave
+

Simulate the exit wave from the sample

+
parakeet simulate exit_wave [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE]
+                            [-d {cpu,gpu}] [--nproc NPROC] [--gpu_id GPU_ID]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-e, --exit_wave
+

The filename for the exit wave

+

Default: “exit_wave.h5”

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
+
+
+
+
optics
+

Simulate the optics and infinite dose image

+
parakeet simulate optics [-h] -c CONFIG [-d {cpu,gpu}] [--nproc NPROC]
+                         [--gpu_id GPU_ID] [-e EXIT_WAVE] [-o OPTICS]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
-e, --exit_wave
+

The filename for the exit wave

+

Default: “exit_wave.h5”

+
+
-o, --optics
+

The filename for the optics

+

Default: “optics.h5”

+
+
+
+
+
+
image
+

Simulate the noisy detector image

+
parakeet simulate image [-h] -c CONFIG [-o OPTICS] [-i IMAGE]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-o, --optics
+

The filename for the optics

+

Default: “optics.h5”

+
+
-i, --image
+

The filename for the image

+

Default: “image.h5”

+
+
+
+
+
+
ctf
+

Simulate the ctf

+
parakeet simulate ctf [-h] -c CONFIG [-o OUTPUT]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-o
+

The filename for the output

+

Default: “ctf.h5”

+
+
+
+
+
+
+
+
analyse
+

Commands to analyse the simulated data

+
parakeet analyse [-h]
+                 {reconstruct,correct,average_particles,average_all_particles,extract,refine}
+                 ...
+
+
+
+
Positional Arguments
+
+
analyse_command
+

Possible choices: reconstruct, correct, average_particles, average_all_particles, extract, refine

+

The parakeet analyse sub commands

+
+
+
+
+
Sub-commands
+
+
reconstruct
+

Reconstruct the volume

+
parakeet analyse reconstruct [-h] -c CONFIG [-d {cpu,gpu}] [-i IMAGE] [-r REC]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
-i, --image
+

The filename for the image

+

Default: “image.mrc”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
+
+
+
+
correct
+

3D CTF correction of the images

+
parakeet analyse correct [-h] -c CONFIG [-i IMAGE] [-cr CORRECTED]
+                         [-ndf NUM_DEFOCUS] [-d {cpu,gpu}]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-i, --image
+

The filename for the image

+

Default: “image.mrc”

+
+
-cr, --corrected
+

The filename for the corrected image

+

Default: “corrected_image.mrc”

+
+
-ndf, --num-defocus
+

Number of defoci that correspond to different depths through for which the sample will be 3D CTF corrected

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
+
+
+
+
average_particles
+

Perform sub tomogram averaging

+
parakeet analyse average_particles [-h] -c CONFIG [-s SAMPLE] [-r REC]
+                                   [-h1 HALF1] [-h2 HALF2]
+                                   [-psz PARTICLE_SIZE] [-n NUM_PARTICLES]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
-h1, --half1
+

The filename for the particle average

+

Default: “half1.mrc”

+
+
-h2, --half2
+

The filename for the particle average

+

Default: “half2.mrc”

+
+
-psz, --particle_size
+

The size of the particles extracted (px)

+

Default: 0

+
+
-n, --num_particles
+

The number of particles to use

+

Default: 0

+
+
+
+
+
+
average_all_particles
+

Perform sub tomogram averaging

+
parakeet analyse average_all_particles [-h] -c CONFIG [-s SAMPLE] [-r REC]
+                                       [-avm AVERAGE] [-psz PARTICLE_SIZE]
+                                       [-n NUM_PARTICLES]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
-avm, --average_map
+

The filename for the particle average

+

Default: “average_map.mrc”

+
+
-psz, --particle_size
+

The size of the particles extracted (px)

+

Default: 0

+
+
-n, --num_particles
+

The number of particles to use

+

Default: 0

+
+
+
+
+
+
extract
+

Perform sub tomogram extraction

+
parakeet analyse extract [-h] -c CONFIG [-s SAMPLE] [-r REC] [-pm PARTICLES]
+                         [-psz PARTICLE_SIZE] [-psm PARTICLE_SAMPLING]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “rec.mrc”

+
+
-pm, --particle_map
+

The filename for the particle average

+

Default: “particle_map.h5”

+
+
-psz, --particle_size
+

The size of the particles extracted (px)

+

Default: 0

+
+
-psm, --particle_sampling
+

The sampling of the particle volume (factor of 2)

+

Default: 1

+
+
+
+
+
+
refine
+

Refine map and model

+
parakeet analyse refine [-h] -c CONFIG [-s SAMPLE] [-r REC]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-r, --rec
+

The filename for the reconstruction

+

Default: “half1.mrc”

+
+
+
+
+
+
+
+
metadata
+

Commands to manipulate metadata

+
parakeet metadata [-h] {export} ...
+
+
+
+
Positional Arguments
+
+
metadata_command
+

Possible choices: export

+

The parakeet metadata sub commands

+
+
+
+
+
Sub-commands
+
+
export
+

Export the metadata to star files for downstream processing

+
parakeet metadata export [-h] [-c CONFIG] [-s SAMPLE] [-i IMAGE]
+                         [--directory DIRECTORY] [--relion RELION]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+

Default: “config.yaml”

+
+
-s, --sample
+

The filename for the sample file

+

Default: “sample.h5”

+
+
-i, --image
+

The filename for the image file

+

Default: “image.h5”

+
+
--directory
+

The directory to export to

+

Default: “.”

+
+
--relion
+

Export the relion metadata

+

Default: True

+
+
+
+
+
+
+
+
pdb
+

Commands to operate on pdb files

+
parakeet pdb [-h] {get,read} ...
+
+
+
+
Positional Arguments
+
+
pdb_command
+

Possible choices: get, read

+

The parakeet pdb sub commands

+
+
+
+
+
Sub-commands
+
+
get
+

Get a PDB file

+
parakeet pdb get [-h] [-d DIRECTORY] id
+
+
+
+
Positional Arguments
+
+
id
+

The PDB ID

+
+
+
+
+
Named Arguments
+
+
-d, --directory
+

The directory to save to

+

Default: “.”

+
+
+
+
+
+
read
+

Read a PDB file

+
parakeet pdb read [-h] filename
+
+
+
+
Positional Arguments
+
+
filename
+

The path to the PDB file

+
+
+
+
+
+
+
+
export
+

Export images to a different format

+
parakeet export [-h] -o OUTPUT [--rot90 ROT90]
+                [--rotation_range ROTATION_RANGE | --select_images SELECT_IMAGES]
+                [--roi ROI]
+                [--complex_mode {complex,real,imaginary,amplitude,phase,phase_unwrap,square,imaginary_square}]
+                [--interlace INTERLACE] [--rebin REBIN]
+                [--filter_resolution FILTER_RESOLUTION]
+                [--filter_shape {square,gaussian}] [--vmin VMIN] [--vmax VMAX]
+                [--sort {angle}]
+                filename
+
+
+
+
Positional Arguments
+
+
filename
+

The input filename

+
+
+
+
+
Named Arguments
+
+
-o, --output
+

The output filename

+
+
--rot90
+

Rotate the image 90deg counter clockwise

+

Default: False

+
+
--rotation_range
+

Select a rotation range (deg).

+

Multiple rotation ranges can be specified as: +–rotation_range=start1,stop1;start2,stop2

+
+
--select_images
+

Select a range of images (start,stop,step)

+
+
--roi
+

Select a region of interest (–roi=x0,y0,x1,y1)

+
+
--complex_mode
+

Possible choices: complex, real, imaginary, amplitude, phase, phase_unwrap, square, imaginary_square

+

How to treat complex numbers

+

Default: “complex”

+
+
--interlace
+

Interlace the scan. If the value <= 1 then the images are kept in the same order, otherwise, the images are reordered by skipping images. For example, if –interlace=2 is set then the images will be written out as [1, 3, 5, … , 2, 4, 6, …]

+
+
--rebin
+

The rebinned factor. The shape of the output images will be original_shape / rebin

+

Default: 1

+
+
--filter_resolution
+

The resolution of the filter (A)

+
+
--filter_shape
+

Possible choices: square, gaussian

+

The shape of the filter

+
+
--vmin
+

The minimum pixel value when exporting to an image

+
+
--vmax
+

The maximum pixel value when exporting to an image

+
+
--sort
+

Possible choices: angle

+

Sort the images

+
+
+
+
+
+
run
+

Run full simulation experiment

+
parakeet run [-h] -c CONFIG [-s SAMPLE] [-e EXIT_WAVE] [-o OPTICS] [-i IMAGE]
+             [-d {cpu,gpu}] [--nproc NPROC] [--gpu_id GPU_ID]
+             [--steps {all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} [{all,sample,sample.new,sample.add_molecules,simulate,simulate.exit_wave,simulate.optics,simulate.image} ...]]
+
+
+
+
Named Arguments
+
+
-c, --config
+

The yaml file to configure the simulation

+
+
-s, --sample
+

The filename for the sample

+

Default: “sample.h5”

+
+
-e, --exit_wave
+

The filename for the exit wave

+

Default: “exit_wave.h5”

+
+
-o, --optics
+

The filename for the optics

+

Default: “optics.h5”

+
+
-i, --image
+

The filename for the image

+

Default: “image.h5”

+
+
-d, --device
+

Possible choices: cpu, gpu

+

Choose the device to use

+
+
--nproc
+

The number of processes to use

+
+
--gpu_id
+

The GPU ids (must match number of processors)

+
+
--steps
+

Possible choices: all, sample, sample.new, sample.add_molecules, simulate, simulate.exit_wave, simulate.optics, simulate.image

+

Which simulation steps to run

+
+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file