Merge pull request #26 from schuenke/dev

Merge of dev (Release 0.6.0)

README.md

@@ -1,88 +1,87 @@
 # Bloch-McConnell (BMC) Simulation Tool
 
-This repository contains a purely python-based Bloch-McConnell (BMC) simulation tool that can be used to simulate 
+This repository contains a purely python-based Bloch-McConnell (BMC) simulation tool that can be used to simulate
 the evolution of the magnetization in various (exchanging) magnetic environments ('pools') under arbitrary
-radio-frequency (RF) irradiation. The tool was developed to simulate Chemical Exchange Saturation Transfer (CEST) or 
-related spectra, but can be used for many other MR simulations as well. 
+radio-frequency (RF) irradiation. The tool was developed to simulate Chemical Exchange Saturation Transfer (CEST) or
+related spectra, but can be used for many other MR simulations as well.
 
 The BMCTool utilizes the [pulseq](https://pulseq.github.io/) open file format to define and store all events (RF pulses,
-gradients, delays, ADCs) that shall be simulated. The scanner settings and characteristic properties of the magnetic 
+gradients, delays, ADCs) that shall be simulated. The scanner settings and characteristic properties of the magnetic
 environments (relaxation times, pool size fractions, exchange rates) are defined and stored in config-files in the
-[YAML](https://yaml.org) file format. 
+[YAML](https://yaml.org) file format.
 
-Every simulation requires exactly one seq-file (containing all events) and at least one config-file. 
+Every simulation requires exactly one seq-file (containing all events) and at least one config-file.
 
 ## Installation
+
 The BMCTool can be installed from [PyPi](https://pypi.org/) using
 
 ``
 pip install bmctool
 ``
 
-### IMPORTANT NOTE FOR RELEASE v0.5.0
-Version 0.5.0 of BMCTool requires PyPulseq >= 1.4.0, which is currently only available if installed directly from the [Dev branch](https://github.com/imr-framework/pypulseq/tree/dev) of the [PyPulseq Github Repository](https://github.com/imr-framework/pypulseq). A working version can be installed using
-
-
-``
-pip install git+https://github.com/imr-framework/pypulseq@c644fd9
-``
-
-A new version of the BMCTool with updated dependencies will be released as soon as PyPulseq v. 1.4.0 is officially released!
-
 ### Initial Test
-To make sure that the installation was successful, you can run an example simulation that is provided with both, 
+
+To make sure that the installation was successful, you can run an example simulation that is provided with both,
 the installation using pip and GitHub. To run an example simulation, simply execute the following code:
+
 ```python
 from bmctool.simulate import sim_example
 sim_example()
 ```
+
 The sim_example function uses the [WASABI.seq](bmctool/library/seq-library/WASABI.seq)
 and [config_wasabi.yaml](bmctool/library/sim-library/config_wasabi.yaml) example files. The generated plot should look
 like this:
 
 ![](https://raw.githubusercontent.com/schuenke/BMCTool/master/examples/example_wasabi_spectrum.png "Example WASABI spectrum")
 
 ## Starting a Simulation
-All simulations using the BMCTool require a config file (in the *yaml* format) that includes all simulation settings 
-and a sequence file (in the *seq* format), which defines the events to be simulated. An 
-[example seq-file](bmctool/library/seq-library/WASABI.seq) and an 
-[example yaml file](bmctool/library/sim-library/config_wasabi.yaml) can be found in the [library](bmctool/library) 
-subfolder. For more information about config and sequence files and about the 
-[pulseq-cest-library](library/pulseq-cest-library), where both types of files are shared, please read the 
+
+All simulations using the BMCTool require a config file (in the *yaml* format) that includes all simulation settings
+and a sequence file (in the *seq* format), which defines the events to be simulated. An
+[example seq-file](bmctool/library/seq-library/WASABI.seq) and an
+[example yaml file](bmctool/library/sim-library/config_wasabi.yaml) can be found in the [library](bmctool/library)
+subfolder. For more information about config and sequence files and about the
+[pulseq-cest-library](library/pulseq-cest-library), where both types of files are shared, please read the
 **Pulseq-CEST Library** section below.
 
-If you created your own files or downloaded them from the [pulseq-cest-library](https://github.com/kherz/pulseq-cest-library), 
+If you created your own files or downloaded them from the [pulseq-cest-library](https://github.com/kherz/pulseq-cest-library),
 you can start the simulation by running the following code:
+
 ```python
 from bmctool.simulate import simulate
 config_path = '<path_to_your_config>'  # can be a str or a Path
 seq_path = '<path_to_your_sequence>'  # can be a str or a Path
 sim = simulate(config_file=config_path, seq_file=seq_path, show_plot=True)
 ```
+
 The simulate function accepts several additional keyword arguments (**kwargs), that allow to adjust the plot.
-These are for example _normalize_ (bool: toggle normalization), _norm_threshold_ (value/list/array: threshold for
-normalization offsets), _offsets_ (list/array: manually defined x-values), _invert_ax_ (bool: toggle invert ax), 
-_plot_mtr_asym_ (bool:toggle plot MTR_asym) and _title_, _x_label_, _y_label_ to control the lables.
+These are for example *normalize* (bool: toggle normalization), *norm_threshold* (value/list/array: threshold for
+normalization offsets), *offsets* (list/array: manually defined x-values), *invert_ax* (bool: toggle invert ax),
+*plot_mtr_asym* (bool:toggle plot MTR_asym) and *title*, *x_label*, *y_label* to control the lables.
 
-The [examples folder](examples) in the [BMCTool GitHub repository](https://github.com/schuenke/BMCTool) contains some 
-further simulation examples as well as an example script to create your own _WASABI.seq_ file. _Please note that this
+The [examples folder](examples) in the [BMCTool GitHub repository](https://github.com/schuenke/BMCTool) contains some
+further simulation examples as well as an example script to create your own *WASABI.seq* file. _Please note that this
 file will include an additional normalization offset at -300 ppm. To use this for normalization in the simulation,
-simply add the kewword argument ``normalize=True`` to the simulate function._ 
+simply add the kewword argument ``normalize=True`` to the simulate function._
 
 ## Pulseq-CEST Project
+
 The BMCTool was developed in parallel to the [pulseq-cest project](https://pulseq-cest.github.io/) that aims to provide
-published and approved CEST saturation blocks in the [pulseq](https://pulseq.github.io/) open file format to enable an 
+published and approved CEST saturation blocks in the [pulseq](https://pulseq.github.io/) open file format to enable an
 exact comparison of CEST saturation blocks with newly developed or adapted saturation blocks for reproducible research.
 The [pulseq-cest project](https://pulseq-cest.github.io/) provides a [MATLAB implementation](https://github.com/kherz/pulseq-cest)
 and a [python implementation](https://github.com/KerstinHut/pypulseq-cest). The python implementation uses the
 [BMCTool](https://github.com/schuenke/BMCTool) and [pypulseq](https://github.com/imr-framework/pypulseq) for config and
 seq file handling. Both, the MATLAB and python implementation use the same Bloch-McConnell equation solver implemented
-in C++, which is much faster than the solver implemented in the BMCTool itself. For extensive simulations we thus 
+in C++, which is much faster than the solver implemented in the BMCTool itself. For extensive simulations we thus
 recommend checking out the [pulseq-cest implementations](https://pulseq-cest.github.io/).
 
 ### Pulseq-CEST Library
-You will find several pre-defined and approved CEST pre-saturation schemes and simulation configs in the 
-[pulseq-cest-library GitHub repository](https://github.com/kherz/pulseq-cest-library). You can clone the library using 
+
+You will find several pre-defined and approved CEST pre-saturation schemes and simulation configs in the
+[pulseq-cest-library GitHub repository](https://github.com/kherz/pulseq-cest-library). You can clone the library using
 
 ``
 git clone https://github.com/kherz/pulseq-cest-library.git

bmctool/__init__.py

@@ -0,0 +1 @@
+GAMMA_HZ = 42.5764