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docs/_sources/api.rst.txt

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+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__

docs/_sources/configuration.rst.txt

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+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

docs/_sources/index.rst.txt

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+.. 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`