diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml index a12035f..1d0c1d7 100755 --- a/.github/workflows/documentation.yaml +++ b/.github/workflows/documentation.yaml @@ -23,14 +23,17 @@ jobs: with: python-version: '3.10' + - name: Install Poetry + uses: Gr1N/setup-poetry@v8 + with: + poetry-version: '1.8.3' + - name: Install dependencies - run: | - python -m pip install --upgrade pip - python -m pip install -e .[tests,docs] + run: poetry install --extras "tests docs" - - name: Update Sphinx htmls + - name: Build MkDocs documentation run: | - make html + poetry run mkdocs build working-directory: docs - name: Publish to gh-pages @@ -39,7 +42,7 @@ jobs: with: publish_branch: gh-pages # default: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: docs/build/html/ + publish_dir: docs/site force_orphan: true - run: echo "Status of job = ${{ job.status }}." diff --git a/.gitignore b/.gitignore index 2ac6e53..466011b 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,5 @@ junit docs/build docs/source/generated docs/source/sg_execution_times.rst +docs/site +docs/generated diff --git a/README.md b/README.md index 9f3eed0..4546465 100755 --- a/README.md +++ b/README.md @@ -32,6 +32,8 @@ We welcome contributions to OSIPI! To contribute, follow these steps: - Make your changes and commit them with descriptive messages. - Push your changes to your fork. - Submit a pull request to the main OSIPI repository. + +For more details on how to contribute, visit the [Developer Guide](https://osipi.github.io/pypi/developers_guide/index.html). #### As mentioned before, this project is still in the early stages of development. If you'd like to contribute by adding functionality, we recommend opening an issue first to discuss your proposed functionality and the best ways to implement it. ## Details diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100755 index d0c3cbf..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = source -BUILDDIR = build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/about/index.md b/docs/about/index.md new file mode 100644 index 0000000..ddfe3df --- /dev/null +++ b/docs/about/index.md @@ -0,0 +1,12 @@ +# About + +The osipi Library is developed by the **Open Source Initiative for Perfusion Imaging (OSIPI)**, an initiative of the perfusion study group of the **International Society for Magnetic Resonance in Medicine (ISMRM)**. + +The osipi package structure and logic follow the lexicon defined by OSIPI, and wrap around selected implementations collected in the code contributions of OSIPI. + +## Scope + +osipi currently only includes methods for the dynamic contrast (DC) approach to perfusion MRI (DC-MRI, a unifying term for the separate fields DCE-MRI and DSC-MRI). In particular, arterial spin labelling (ASL) solutions are not currently included, but this may change in the future. + +!!! note "Future Updates" + The inclusion of arterial spin labelling (ASL) solutions may change in the future. diff --git a/docs/source/developers_guide/index.rst b/docs/contribution/index.md old mode 100755 new mode 100644 similarity index 51% rename from docs/source/developers_guide/index.rst rename to docs/contribution/index.md index c879b92..8dc5d64 --- a/docs/source/developers_guide/index.rst +++ b/docs/contribution/index.md @@ -1,29 +1,56 @@ -.. _developer-guide: - -############### -Developer guide -############### +# Developer Guide There are multiple ways to contribute to `osipi` and we welcome them all. `osipi` is a tool developed by the research community for the research community, and we are all responsible for ensuring it is as good as it can be. So, if you feel some part of it is not, fix it! -The way to do this is by making a pull request on github. If you are not familiar with github pull requests, it is not as scary as it sounds. The simplest way is to find the file that you want to edit on gtihub in your browser, edit it manually and follow the prompts to create a fork and pull request. +The way to do this is by making a pull request on GitHub. If you are not familiar with GitHub pull requests, it is not as scary as it sounds. The simplest way is to find the file that you want to edit on GitHub in your browser, edit it manually and follow the prompts to create a fork and pull request. + +## Making a Pull Request (PR) to the OSIPI Package +### Step 1: Fork the Repository +First, fork the OSIPI repository to your GitHub account and make a new branch with the your new feature or bug fix. + +### Step 2: Set Up Your Development Environment +After creating a fork, you have two options: +#### Option 1: Use Poetry + +1. **Install Poetry**: If you don't have Poetry installed, follow the instructions [here](https://python-poetry.org/docs/#installation). +2. **Install Dependencies**: Run the following command in your terminal: + ```sh + poetry install + ``` +#### Option 2: Use Requirements File + +1. **Install Dependencies**: Run the following command in your terminal: + ```sh + pip install -r requirements.txt + ``` + +### Step 3: Make Your Contribution +Make your changes or add your contribution to the codebase. -************************** -How to contribute examples -************************** +### Step 4: Run Pre-commit Checks +Before pushing your changes, run pre-commit checks to ensure your code meets the project's standards. + +1. Run the following command in your terminal: + ```sh + pre-commit run --all-files + ``` + +### Step 5: Push Your Changes and Create a PR +1. Push your changes to your forked repository. +2. Create a pull request (PR) to the main OSIPI repository. + + +## How to Contribute Examples One way to contribute is by providing examples of how you used `osipi` for a specific task. These are usually real-world examples with a relevant aim, perhaps to derive some results that you have published. To package these up as an example, follow these steps: -1. Code up your example in a single python file in a narrative style, similar to a notebook. Have a look at the current examples to see how these need to be formatted, especially thier docstrings, to make sure they show up properly on the website. +1. Code up your example in a single Python file in a narrative style, similar to a notebook. Have a look at the current examples to see how these need to be formatted, especially their docstrings, to make sure they show up properly on the website. 2. When you save your file, make sure the filename starts with *plot_*. -3. Then drop your file in the examples folder `osipi-docs-examples` in the appropriate subolder. +3. Then drop your file in the examples folder `osipi-docs-examples` in the appropriate subfolder. When the documentation is generated, your example will automatically appear in the examples gallery and also in the documentation of any function you are using in the example. - -******************************* -How to contribute documentation -******************************* +## How to Contribute Documentation `osipi` is a user interface and for that reason good, clear and well-structured documentation is equally important as the quality of the functionality itself. We especially welcome suggestions for improving the documentation from end-users who are not necessarily contributing new code. You know best what works, and what doesn't. @@ -31,92 +58,63 @@ If you are a user of `osipi`, and some part of the documentation is not as clear If you want to edit the documentation of a specific function, then you need to find the function in the osipi source code `osipi-src`. Find the function and edit the documentation string immediately below its definition. If you want to edit any other part of the documentation, find the appropriate file in the documentation source code `osipi-docs-source` and edit it there. +## How to Contribute Tests -*********************** -How to contribute tests -*********************** - -Beyond documentation and functionality, solid testing is equally critical for ensuring long-term stability of a package. `osipi` uses a continuous integration model where all tests are run before each push to the central repository. This is important because often changes at one part of the code, even if tested well locally, can have unintended consequences at other parts. The testing prevents that these errors propagate and destablize parts of the package. +Beyond documentation and functionality, solid testing is equally critical for ensuring long-term stability of a package. `osipi` uses a continuous integration model where all tests are run before each push to the central repository. This is important because often changes at one part of the code, even if tested well locally, can have unintended consequences at other parts. The testing prevents that these errors propagate and destabilize parts of the package. If you find a bug in any part of the code, this obviously points to a flaw in the code, but it also reveals a gap in the testing. It is critical when this happens that both the code AND the tests are reviewed to ensure that in future a scenario of this type is picked up during testing. The tests are defined in the folder `osipi-tests`. - -******************************* -How to contribute functionality -******************************* +## How to Contribute Functionality OSIPI is always happy to receive new functionality for inclusion in the `osipi` package. This can be code that addresses a gap in the current functionality, or it can be code that improves the performance of a current implementation. Improvements can consist of extending the functionality (e.g. with new optional arguments), user friendliness or consistency, improvement of the accuracy or precision in the results, computation time, or platform independence, or improved documentation or code structure. -Contribution of functionality generally proceeds in two steps. In the first step you submit your code to the primary *contributions* repository as explained in its `wiki `_. The task force will catalogue your code in the contributions repository and test it as explained in the `guidance `_. Afterwards, if it is found to address a gap in `osipi` and/or improve existing functionality, you will be invited to submit a pull request to `osipi` containing your contribution formatted as required by the package. +Contribution of functionality generally proceeds in two steps. In the first step you submit your code to the primary *contributions* repository as explained in its [wiki](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki/How-to-contribute-code). The task force will catalogue your code in the contributions repository and test it as explained in the [guidance](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki/The-testing-approach). Afterwards, if it is found to address a gap in `osipi` and/or improve existing functionality, you will be invited to submit a pull request to `osipi` containing your contribution formatted as required by the package. While this is the general process, we accept there may be situations where a new submission to the contributions repository is overkill, for instance if your improvement concerns documentation only, or improvements in code structure or style. In that case a direct pull request to `osipi` may be acceptable - when in doubt please contact the OSIPI repository lead in the first instance to avoid unnecessary work. -See section on design principles below for general requirements from `osipi` code snippets. - - -************************ -How to contribute issues -************************ - -If you have a constructive suggestion for how `osipi` can be improved, but you are not able to address it yourself for some reason, it is still extremely helpful if you write this up as an issue so it can be picked up by others at a later stage. To write up an issue, go to the `osipi` repository on github, select `issues` and write a new one. Make sure to provide sufficient detail so that others can understand and address the issue. +See the section on design principles below for general requirements from `osipi` code snippets. +## How to Contribute Issues -***************** -Design principles -***************** +If you have a constructive suggestion for how `osipi` can be improved, but you are not able to address it yourself for some reason, it is still extremely helpful if you write this up as an issue so it can be picked up by others at a later stage. To write up an issue, go to the `osipi` repository on GitHub, select `issues` and write a new one. Make sure to provide sufficient detail so that others can understand and address the issue. -Style guide -^^^^^^^^^^^ +## Design Principles -`osipi` follows the `google python style guide `_. This means especially also that we expect proper attention to error handling. Consider for instance what happens if a user calls your snippet using arguments of incorrect type or length. Will they get an appropriate error message that will help them identify and fix the error? +### Style Guide +`osipi` follows the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html). This means especially also that we expect proper attention to error handling. Consider for instance what happens if a user calls your snippet using arguments of incorrect type or length. Will they get an appropriate error message that will help them identify and fix the error? -Package structure -^^^^^^^^^^^^^^^^^ +### Package Structure -The `osipi` documentation follows the structure of the OSIPI Lexicon exactly - see `here `_ for a detailed description of the Lexicon. +The `osipi` documentation follows the structure of the OSIPI Lexicon exactly - see [here](https://osipi.github.io/OSIPI_CAPLEX/) for a detailed description of the Lexicon. -From a user perspective, the package structure is a flat list of functions that can all be accessed as `osipi.some_function`. They are listed in the __init__ file of the package, directly under the folder `src\osipi`. For clarity the code itself is organised into modules, but these may evolve over time and should not be accessed directly. Module names all start with an underscore `_module.py` to emphasise their private and transient nature. Equally, subfolders may be added in the future as the package grows. +From a user perspective, the package structure is a flat list of functions that can all be accessed as `osipi.some_function`. They are listed in the __init__ file of the package, directly under the folder `src\osipi`. For clarity, the code itself is organized into modules, but these may evolve over time and should not be accessed directly. Module names all start with an underscore `_module.py` to emphasize their private and transient nature. Equally, subfolders may be added in the future as the package grows. -:: - src - └── osipi - ├── __init__.py - ├── _module_1.py - ├── _module_2.py - ├── - └── _module_n.py +### Code Snippets +`osipi` is a collection of *simple* code snippets following a *simple* functional programming paradigm (did you see how we said *simple* twice there?). Each code snippet is a Python function that takes OSIPI variables as arguments and returns other OSIPI variables as results. At this stage, we are *not* planning to include an object-oriented interface or internal logic as this reduces the modularity of the code snippets, reduces compatibility with other packages, and increases the overhead of learning how to use `osipi`. Therefore, all code contributions will essentially consist of a new function or an improvement of an existing function. -Code snippets -^^^^^^^^^^^^^ +Beyond the general requirements of the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html), `osipi` requires that each new function is accompanied by an appropriate test in the tests folder, and that each function fully conforms to the Lexicon. In particular: -`osipi` is a collection of *simple* code snippets following a *simple* functional programming paradigm (did you see how we said *simple* twice there?). Each code snippet is a python function that takes OSIPI variables as argument and returns other OSIPI variables as result. At this stage we are *not* planning to include an object oriented interface or internal logic as this reduces the modularity of the code snippets, reduces compatibility with other packages and increases the overhead of learning how to use `osipi`. Therefore all code contributions will essentially exist of a new function, or an improvement of an existing function. - -Beyond the general requirements of the `google python style guide `_, `osipi` requires that each new function is accompanied by an appropriate test in the tests folder, and that each function fully conforms to the Lexicon. In particular: - -1. Each function must be defined in the lexicon, and the doc string must include a reference section containing the following four items: - - Lexicon url: webpage in the Lexicon where the function is defined. +1. Each function must be defined in the lexicon, and the docstring must include a reference section containing the following four items: + - Lexicon URL: webpage in the Lexicon where the function is defined. - Lexicon code: machine-readable code identifying the entry in the Lexicon. - OSIPI name: human-readable name for the function as defined in the Lexicon. - Adapted from contribution: module.py in the original snippet in the code contribution repository -2. Each argument to the function as as well as each return value *must* be defined in the Lexicon. The doc string of the function must provide the following data on each argument and return value: - - python data type (include type hint in the function definition) - - Lexicon code: machine-readable code identifying the corresponding quantitity in the Lexicon. +2. Each argument to the function as well as each return value *must* be defined in the Lexicon. The docstring of the function must provide the following data on each argument and return value: + - Python data type (include type hint in the function definition) + - Lexicon code: machine-readable code identifying the corresponding quantity in the Lexicon. - OSIPI name: human-readable name for the quantity as defined in the Lexicon. 3. All arguments and return values must be provided in OSIPI units as defined in the Lexicon. 4. Arguments should be provided using OSIPI notation as defined in the Lexicon. -5. The docstring of the function must contain a self contained code example that runs the function and illustrates the output. - - -.. note:: +5. The docstring of the function must contain a self-contained code example that runs the function and illustrates the output. +!!!note If your function addresses entirely novel functionality or uses new variables that are not yet described in the Lexicon, then you should first contact the Lexicon maintainers and request that it is added as an entry to the Lexicon. Only afterwards can it be considered as a contribution to the `osipi` package. -.. note:: - - The original `library for code contributions `_ is less stringent as to code structure and documentation or testing requirements. However, it is nevertheless advisable to adhere to the same guidelines when submitting code to the original contributions repository as this will make it easier for testers to understand and run your code, and it will reduce the overhead on your part in rewriting the code if it is subsequently invited as a contribution to `osipi`. +!!!note + The original [library for code contributions](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki/How-to-contribute-code) is less stringent as to code structure and documentation or testing requirements. However, it is nevertheless advisable to adhere to the same guidelines when submitting code to the original contributions repository as this will make it easier for testers to understand and run your code, and it will reduce the overhead on your part in rewriting the code diff --git a/docs/examples/.DS_Store b/docs/examples/.DS_Store deleted file mode 100644 index 6f81a2f..0000000 Binary files a/docs/examples/.DS_Store and /dev/null differ diff --git a/docs/examples/README.md b/docs/examples/README.md new file mode 100644 index 0000000..7e371c4 --- /dev/null +++ b/docs/examples/README.md @@ -0,0 +1,5 @@ + +# Examples + + +### Illustrating common use cases of osipi. diff --git a/docs/examples/README.rst b/docs/examples/README.rst deleted file mode 100755 index adff135..0000000 --- a/docs/examples/README.rst +++ /dev/null @@ -1,5 +0,0 @@ -######## -Examples -######## - -Illustrating common use cases of osipi. diff --git a/docs/examples/aif/README.rst b/docs/examples/aif/README.md old mode 100755 new mode 100644 similarity index 100% rename from docs/examples/aif/README.rst rename to docs/examples/aif/README.md diff --git a/docs/examples/aif/plot_aif_parker.py b/docs/examples/aif/plot_aif_parker.py old mode 100755 new mode 100644 diff --git a/docs/examples/aif/plot_dummy.py b/docs/examples/aif/plot_dummy.py old mode 100755 new mode 100644 diff --git a/docs/examples/signal/plot_signal_SPGR.py b/docs/examples/signal/plot_signal_SPGR.py deleted file mode 100644 index 0e4b59d..0000000 --- a/docs/examples/signal/plot_signal_SPGR.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -============== -Linear model for relationship between R1 and magnitude signal -============== - -Demonstrating the linear model for relationship between R1 and magnitude signal, s = k.R1 -""" - -# %% -# Import necessary packages -import matplotlib.pyplot as plt -import numpy as np -import osipi - -# %% -# Convert a series of R1 values to the corresponding signal intensities using the SPGR model. - -R1 = np.linspace(0.1, 10, 50) # R1 in units of /s. -S0 = np.float64(100) # fully T1-relaxed signal in a.u. -TR = np.float64(5e-3) # repetition time in units of s. -a = np.float64(15) # prescribed flip angle in units of deg. -S = osipi.signal_SPGR(R1, S0, TR, a) # signal in a.u. -print(f"Signal: {S}") - -# Plot S vs. R1 -plt.plot(R1, S, "r-") -plt.xlabel("R1 (/s)") -plt.ylabel("S (a.u.)") -plt.show() diff --git a/docs/examples/signal/plot_signal_linear.py b/docs/examples/signal/plot_signal_linear.py deleted file mode 100644 index 5702d8b..0000000 --- a/docs/examples/signal/plot_signal_linear.py +++ /dev/null @@ -1,27 +0,0 @@ -""" -============== -Linear model for relationship between R_1 and magnitude signal S -============== - -Demonstrating the linear model for relationship between R_1 and magnitude signal, S = k.R_1 -""" - -# %% -# Import necessary packages -import matplotlib.pyplot as plt -import numpy as np -import osipi - -# %% -# Convert a series of R1 values to the corresponding signal intensities. - -R1 = np.array([0.0, 1.5, 3.0, 4.0, 10.0]) # R_1 in units of /s -k = np.float64(150.0) # constant of proportionality in units of a.u. s -S = osipi.signal_linear(R1, k) # signal in a.u. -print(f"Signal: {S}") - -# Plot S vs. R1 -plt.plot(R1, S, "ro-") -plt.xlabel("R1 (/s)") -plt.ylabel("S (a.u.)") -plt.show() diff --git a/docs/examples/signal_to_concentration/plot_signal_to_concentration_R1_to_C_linear_relaxivity.py b/docs/examples/signal_to_concentration/plot_signal_to_concentration_R1_to_C_linear_relaxivity.py deleted file mode 100644 index e39f271..0000000 --- a/docs/examples/signal_to_concentration/plot_signal_to_concentration_R1_to_C_linear_relaxivity.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -============== -Electromagnetic property inverse model: longitudinal relaxation rate, linear with relaxivity -============== - -Demonstrating the inverse linear relaxivity model - for converting R_1 to tissue indicator concentration C. -""" - -# %% -# Import necessary packages -import matplotlib.pyplot as plt -import numpy as np -import osipi - -# %% -# Convert a series of R1 values to the corresponding indicator concentrations. -R1 = np.array([1, 2, 3, 4, 5, 6], dtype=np.float64) -R10 = np.float64(1) -r1 = np.float64(5) - -C = osipi.R1_to_C_linear_relaxivity(R1, R10, r1) -print(f"Concentration (mM): {C}") - -# Plot C vs. R1 -plt.plot(R1, C, "r-") -plt.xlabel("R1 (/s)") -plt.ylabel("C (mM)") -plt.show() diff --git a/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_C_via_R1_SPGR.py b/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_C_via_R1_SPGR.py deleted file mode 100644 index b461275..0000000 --- a/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_C_via_R1_SPGR.py +++ /dev/null @@ -1,69 +0,0 @@ -""" -============== -Signal to concentration via electromagnetic property (SPGR, FXL, analytical linear relaxivity) -============== - -Demonstrating the SPGR model for relationship between - signal S and total tissue indicator concentration, assuming the FXL. -""" - -# %% -# Import necessary packages -import matplotlib.pyplot as plt -import numpy as np -import osipi - -# %% -# Convert a series of S values to the corresponding indicator concentrations. -# Example data adapted from OSIPI repository ("vox_1") -S = np.array( - [ - 7, - 9, - 6, - 10, - 9, - 6, - 9, - 10, - 9, - 9, - 9, - 12, - 8, - 10, - 12, - 15, - 53, - 70, - 71, - 70, - 63, - 58, - 54, - 50, - 53, - 48, - 52, - 49, - 42, - ], - dtype=np.float64, -) -S_baseline = S[0] # use first point for baseline signal -R10 = np.float64(1 / 1.4) -TR = np.float64(0.002) -a = np.float64(13) -r1 = np.float64(4.5) - -C = osipi.S_to_C_via_R1_SPGR(S, S_baseline, R10, TR, a, r1) -print(f"Concentration (mM): {C}") - -# Plot S and C -fig, ax = plt.subplots(2, 1) -ax[0].plot(S, "b-") -ax[0].set_ylabel("S (a.u.)") -ax[1].plot(C, "b-") -ax[1].set_ylabel("C (mM)") -ax[1].set_xlabel("time point") -plt.show() diff --git a/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_R1_SPGR.py b/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_R1_SPGR.py deleted file mode 100644 index 27f2e83..0000000 --- a/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_R1_SPGR.py +++ /dev/null @@ -1,67 +0,0 @@ -""" -============== -Signal to electromagnetic properties (R1) (SPGR, FXL, analytical linear relaxivity) -============== - -Demonstrating the SPGR model for relationship between signal S and R1, assuming the FXL. -""" - -# %% -# Import necessary packages -import matplotlib.pyplot as plt -import numpy as np -import osipi - -# %% -# Convert a series of S values to the corresponding R1 values. -# Example data adapted from OSIPI repository ("vox_1") -S = np.array( - [ - 7, - 9, - 6, - 10, - 9, - 6, - 9, - 10, - 9, - 9, - 9, - 12, - 8, - 10, - 12, - 15, - 53, - 70, - 71, - 70, - 63, - 58, - 54, - 50, - 53, - 48, - 52, - 49, - 42, - ], - dtype=np.float64, -) -S_baseline = np.float64(S[0]) # use first point for baseline signal -R10 = np.float64(1 / 1.4) -TR = np.float64(0.002) -a = np.float64(13) - -R1 = osipi.S_to_R1_SPGR(S, S_baseline, R10, TR, a) -print(f"R_1 (/s): {R1}") - -# Plot S and R1 -fig, ax = plt.subplots(2, 1) -ax[0].plot(S, "b-") -ax[0].set_ylabel("S (a.u.)") -ax[1].plot(R1, "b-") -ax[1].set_ylabel("R1 (/s)") -ax[1].set_xlabel("time point") -plt.show() diff --git a/docs/examples/tissue/README.rst b/docs/examples/tissue/README.md old mode 100755 new mode 100644 similarity index 100% rename from docs/examples/tissue/README.rst rename to docs/examples/tissue/README.md diff --git a/docs/examples/tissue/plot_extended_tofts.py b/docs/examples/tissue/plot_extended_tofts.py old mode 100755 new mode 100644 diff --git a/docs/examples/tissue/plot_tofts.py b/docs/examples/tissue/plot_tofts.py old mode 100755 new mode 100644 diff --git a/docs/source/_static/osipi.png b/docs/img/osipi.png old mode 100755 new mode 100644 similarity index 100% rename from docs/source/_static/osipi.png rename to docs/img/osipi.png diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..50037d9 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,27 @@ +# Osipi Documentation + +Welcome to the Osipi documentation! This guide is intended to help you get started with Osipi and provide the information you need to maximize its potential. + +## Warning + +!!! warning + `osipi` is developed in public but is a work in progress. This version contains mostly temporary placeholder functionality. + +## About Osipi + +`osipi` is the authoritative Python package for perfusion MRI. It is developed by the Open Source Initiative for Perfusion Imaging (OSIPI), which is a study group initiative of the International Society for Magnetic Resonance in Medicine (ISMRM). + +## Purpose + +The purpose of `osipi` is to standardize and streamline the use of perfusion MRI, ensuring consistency and reliability across different implementations and studies. The package follows the lexicon defined by OSIPI and integrates selected implementations from the original code contributions made by the OSIPI community. + + +Explore the documentation to learn more about how to use `osipi` and leverage its full capabilities for your perfusion MRI projects. + +## Sections + +- [User Guide](user-guide/index.md) +- [Contribution Guidelines](contribution/index.md) +- [References](references/index.md) +- [About](about/index.md) +- [Examples](examples/index.md) diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100755 index dc1312a..0000000 --- a/docs/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=source -set BUILDDIR=build - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -if "%1" == "" goto help - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/docs/references/index.md b/docs/references/index.md new file mode 100644 index 0000000..5e236db --- /dev/null +++ b/docs/references/index.md @@ -0,0 +1,10 @@ +# Reference + +This reference manual details all functions included in `osipi`, describing what they are and what they do. Documentation of individual functions contains self-contained example code that demonstrates basic usage of the function. + +The `osipi` package currently only includes methods for the dynamic contrast (DC) approach to perfusion MRI (DC-MRI, a unifying term for the separate fields DCE-MRI and DSC-MRI). In particular arterial spin labelling (ASL) solutions are not currently included, but may be added in the future. + +This reference guide, like the `osipi` package itself, adheres closely to the structure and language of the [OSIPI Lexicon](https://osipi.github.io/OSIPI_CAPLEX/). + +!!!warning + `osipi` is in development and this reference guide currently contains mainly empty placeholder entries. diff --git a/docs/references/models.md b/docs/references/models.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/references/models/aif_models/aif_georgiou.md b/docs/references/models/aif_models/aif_georgiou.md new file mode 100644 index 0000000..6cf2330 --- /dev/null +++ b/docs/references/models/aif_models/aif_georgiou.md @@ -0,0 +1,3 @@ +# osipi.aif_georgiou + +::: osipi.aif_georgiou diff --git a/docs/references/models/aif_models/aif_parker.md b/docs/references/models/aif_models/aif_parker.md new file mode 100644 index 0000000..0d6307f --- /dev/null +++ b/docs/references/models/aif_models/aif_parker.md @@ -0,0 +1,20 @@ +# osipi.aif_parker + + +::: osipi.aif_parker + +## Example using `osipi.aif_parker` + +
+ + The Parker AIF - a play with variables +

+ + + The Parker AIF - a play with variables + + + +

+ +
diff --git a/docs/references/models/aif_models/aif_weinmann.md b/docs/references/models/aif_models/aif_weinmann.md new file mode 100644 index 0000000..8c6fa18 --- /dev/null +++ b/docs/references/models/aif_models/aif_weinmann.md @@ -0,0 +1,3 @@ +# osipi.aif_weinmann + +::: osipi.aif_weinmann diff --git a/docs/references/models/aif_models/index.md b/docs/references/models/aif_models/index.md new file mode 100644 index 0000000..adae95a --- /dev/null +++ b/docs/references/models/aif_models/index.md @@ -0,0 +1,5 @@ +# AIF models + +- [aif_parker](aif_parker.md) +- [aif_georgiou](aif_georgiou.md) +- [aif_weinmann](aif_weinmann.md) diff --git a/docs/references/models/index.md b/docs/references/models/index.md new file mode 100644 index 0000000..7cdc134 --- /dev/null +++ b/docs/references/models/index.md @@ -0,0 +1,8 @@ +# Models Overview + + +- [aif_parker](aif_models/aif_parker.md) +- [aif_georgiou](aif_models/aif_georgiou.md) +- [aif_weinmann](aif_models/aif_weinmann.md) +- [tofts](tissue_models/tofts.md) +- [extended_tofts](tissue_models/extended_tofts.md) diff --git a/docs/references/models/tissue_models/extended_tofts.md b/docs/references/models/tissue_models/extended_tofts.md new file mode 100644 index 0000000..b8b974c --- /dev/null +++ b/docs/references/models/tissue_models/extended_tofts.md @@ -0,0 +1,21 @@ +# osipi.extended_tofts + +::: osipi.extended_tofts + +## Example using `osipi.extended_tofts` + + + +
+ + The Extended Tofts model +

+ + + The Extended Tofts model + + + +

+ +
diff --git a/docs/references/models/tissue_models/index.md b/docs/references/models/tissue_models/index.md new file mode 100644 index 0000000..298b575 --- /dev/null +++ b/docs/references/models/tissue_models/index.md @@ -0,0 +1,3 @@ + +- [tofts](tofts.md) +- [extended_tofts](extended_tofts.md) diff --git a/docs/references/models/tissue_models/tofts.md b/docs/references/models/tissue_models/tofts.md new file mode 100644 index 0000000..0dcc063 --- /dev/null +++ b/docs/references/models/tissue_models/tofts.md @@ -0,0 +1,20 @@ +# osipi.tofts + +::: osipi.tofts + +## Example using `osipi.tofts` + + +
+ + The Tofts model +

+ + + The Tofts model + + + +

+ +
diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100755 index 61521a6..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,17 +0,0 @@ -autodocsumm -docutils -myst-parser -pydata-sphinx-theme -sphinx -sphinx-copybutton -sphinx-design -sphinx-remove-toctrees -sphinxcontrib-applehelp -sphinxcontrib-devhelp -sphinxcontrib-htmlhelp -sphinxcontrib-jsmath -sphinxcontrib-qthelp -sphinxcontrib-serializinghtml -#nbsphinx -sphinx-gallery -rstcheck[sphinx] diff --git a/docs/source/.DS_Store b/docs/source/.DS_Store deleted file mode 100644 index 74823c7..0000000 Binary files a/docs/source/.DS_Store and /dev/null differ diff --git a/docs/source/_templates/autosummary.rst b/docs/source/_templates/autosummary.rst deleted file mode 100755 index 7775984..0000000 --- a/docs/source/_templates/autosummary.rst +++ /dev/null @@ -1,32 +0,0 @@ -{{ fullname | escape | underline }} - - -.. currentmodule:: {{ module }} - - -{% if objtype in ['class'] %} -.. auto{{ objtype }}:: {{ objname }} - - :show-inheritance: - :special-members: __call__ - -{% else %} -.. auto{{ objtype }}:: {{ objname }} - -{% endif %} - -{% if objtype in ['class', 'method', 'function'] %} -{% if objname in ['AxesGrid', 'Scalable', 'HostAxes', 'FloatingAxes', - - 'ParasiteAxesAuxTrans', 'ParasiteAxes'] %} - -.. Filter out the above aliases to other classes, as sphinx gallery - creates no example file for those (sphinx-gallery/sphinx-gallery#365) - -{% else %} - -.. minigallery:: {{module}}.{{objname}} - :add-heading: - -{% endif %} -{% endif %} diff --git a/docs/source/about/index.rst b/docs/source/about/index.rst deleted file mode 100755 index 647e2ac..0000000 --- a/docs/source/about/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -##### -About -##### - -``osipi`` is developed by the Open Source Initiative for Perfusion Imaging `OSIPI `_, an initiative of the perfusion study group of the International Society for Magnetic Resonance in Medicine `ISMRM `_. - -The ``osipi`` package structure and logic follows the `lexicon `_ defined by OSIPI, and wraps around selected implementations collected in the `code contributions `_ of OSIPI. - -Scope -^^^^^ - -`osipi` currently only includes methods for the dynamic contrast (DC) approach to perfusion MRI (DC-MRI, a unifying term for the separate fields DCE-MRI and DSC-MRI). In particular arterial spin labelling (ASL) solutions are not currently included, but this may change in the future. diff --git a/docs/source/conf.py b/docs/source/conf.py deleted file mode 100755 index ee5f9f1..0000000 --- a/docs/source/conf.py +++ /dev/null @@ -1,136 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# For the full list of built-in configuration values, see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - -import os - -# -- Project information --------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -import sys - -project = "osipi" -copyright = "2022, OSIPI" -author = "OSIPI" -release = "0.1.1" - -# -- Path setup ------------------------------------------------------ -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like -# shown here - -sys.path.insert(0, os.path.abspath("../../src")) - -# -- General configuration ------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones -extensions = [ - "sphinx.ext.napoleon", # parsing of NumPy and Google style docstrings - "sphinx.ext.autodoc", # sphinx autodocumentation generation - # generates function/method/attribute summary lists - "sphinx.ext.autosummary", - "sphinx.ext.viewcode", # viewing source code - # generate links to the documentation of objects in external - # projects - "sphinx.ext.intersphinx", - "autodocsumm", - "myst_parser", # parser for markdown language - "sphinx_copybutton", # copy button for code blocks - "sphinx_design", # sphinx web design components - "sphinx_remove_toctrees", # selectively remove toctree objects from pages - "sphinx_gallery.gen_gallery", # thumbnail galleries -] - -# Settings for sphinx-gallery, see -# https://sphinx-gallery.github.io/stable/getting_started.html#create-simple-gallery -sphinx_gallery_conf = { - # path to the example scripts relative to conf.py - "examples_dirs": "../examples", - # path to where to save gallery generated output - "gallery_dirs": "generated/examples", - # directory where function/class granular galleries are stored - "backreferences_dir": "generated/backreferences", - # Modules for which function/class level galleries are created. - "doc_module": ("osipi",), - # objects to exclude from implicit backreferences. The default option - # is an empty set, i.e. exclude nothing. - "exclude_implicit_doc": {}, - # thumbnail for examples that do not generate any plot - "default_thumb_file": "_static/osipi.png", - # Disabling download button of all scripts - "download_all_examples": False, -} - -# This way a link to other methods, classes, or modules can be made -# with back ticks so that you don't have to use qualifiers like -# :class:, :func:, :meth: and the likes -default_role = "obj" - -# Add any paths that contain templates here, relative to this -# directory -templates_path = ["_templates"] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path -exclude_patterns = [] - -# -- Extension configuration ----------------------------------------- -# Map intersphinx to pre-exisiting documentation from other projects -# used in this project -intersphinx_mapping = { - "python": ("https://docs.python.org/3/", None), - "numpy": ("https://numpy.org/doc/stable/", None), - "matplotlib": ("https://matplotlib.org/stable/", None), - "pydicom": ("https://pydicom.github.io/pydicom/stable/", None), - "nibabel": ("https://nipy.org/nibabel/", None), - "pandas": ("https://pandas.pydata.org/docs/", None), - "skimage": ("https://scikit-image.org/docs/stable/", None), -} - -autosummary_generate = True # enable autosummary extension - -# Tell sphinx-autodoc-typehints to generate stub parameter annotations -# including types, even if the parameters aren't explicitly -# documented. -always_document_param_types = True - -# Remove auto-generated API docs from sidebars. -remove_from_toctrees = ["_autosummary/*"] - -# -- Options for HTML output ----------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output - -# The theme to use for HTML and HTML Help pages. See the -# documentation for a list of builtin themes -html_theme = "pydata_sphinx_theme" - -html_theme_options = { - "github_url": "https://github.com/OSIPI/pypi", - "collapse_navigation": True, - "use_edit_page_button": True, -} -html_context = { - "github_url": "https://github.com", - "github_user": "OSIPI", - "github_repo": "pypi", - "github_version": "dev", - "doc_path": "docs/source", -} - -# Add any paths that contain custom static files (such as style -# sheets) here, relative to this directory. They are copied after the -# builtin static files, so a file named "default.css" will overwrite -# the builtin "default.css" -html_static_path = ["_static"] - -# The suffix(es) of source filenames. -source_suffix = [".rst", ".md"] - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -html_logo = "_static/osipi.png" diff --git a/docs/source/index.rst b/docs/source/index.rst deleted file mode 100755 index e5fbb99..0000000 --- a/docs/source/index.rst +++ /dev/null @@ -1,28 +0,0 @@ -.. dbdicom documentation master file, created by - sphinx-quickstart on Mon Oct 10 07:46:23 2022. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -################### -osipi documentation -################### - -``osipi`` is the authorative python package for perfusion MRI. - -``osipi`` is developed by the Open Source Initiative for Perfusion Imaging (OSIPI), an initiative of the perfusion study group of the International Society for Magnetic Resonance in Medicine (ISMRM). - -The ``osipi`` package structure and logic follows the lexicon defined by OSIPI, and wraps around selected implementations collected in the original code contributions of OSIPI. - -.. warning:: - - ``osipi`` is developed in public but is work in progress. This version contains mostly temporary placeholder functionalty. - - -.. toctree:: - :maxdepth: 2 - - user_guide/index - reference/index - generated/examples/index - developers_guide/index - about/index diff --git a/docs/source/reference/alphabetical.rst b/docs/source/reference/alphabetical.rst deleted file mode 100755 index d86073c..0000000 --- a/docs/source/reference/alphabetical.rst +++ /dev/null @@ -1,19 +0,0 @@ -Index -^^^^^ - -Alphabetic list of all currently available `osipi` code snippets. - -.. currentmodule:: osipi - - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - aif_georgiou - aif_parker - aif_weinmann - extended_tofts - signal_linear - signal_SPGR - tofts diff --git a/docs/source/reference/general.averaging.rst b/docs/source/reference/general.averaging.rst deleted file mode 100755 index 95c59ee..0000000 --- a/docs/source/reference/general.averaging.rst +++ /dev/null @@ -1,12 +0,0 @@ -Averaging -========= - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/general.convolution.rst b/docs/source/reference/general.convolution.rst deleted file mode 100644 index 0c232cc..0000000 --- a/docs/source/reference/general.convolution.rst +++ /dev/null @@ -1,13 +0,0 @@ -Convolution -^^^^^^^^^^^ - -.. currentmodule:: osipi - -Exponential convolution ------------------------ - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - exp_conv diff --git a/docs/source/reference/general.deconvolution.rst b/docs/source/reference/general.deconvolution.rst deleted file mode 100755 index d03775a..0000000 --- a/docs/source/reference/general.deconvolution.rst +++ /dev/null @@ -1,12 +0,0 @@ -Deconvolution -============= - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/general.descriptive.rst b/docs/source/reference/general.descriptive.rst deleted file mode 100755 index 8d3e5ef..0000000 --- a/docs/source/reference/general.descriptive.rst +++ /dev/null @@ -1,12 +0,0 @@ -Descriptive -=========== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/general.forward.rst b/docs/source/reference/general.forward.rst deleted file mode 100755 index 6c45ceb..0000000 --- a/docs/source/reference/general.forward.rst +++ /dev/null @@ -1,12 +0,0 @@ -Forward -======= - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/general.optimization.rst b/docs/source/reference/general.optimization.rst deleted file mode 100755 index f10864f..0000000 --- a/docs/source/reference/general.optimization.rst +++ /dev/null @@ -1,12 +0,0 @@ -Optimization -============ - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/general.rst b/docs/source/reference/general.rst deleted file mode 100755 index eaf4841..0000000 --- a/docs/source/reference/general.rst +++ /dev/null @@ -1,15 +0,0 @@ -******* -General -******* - -.. toctree:: - :maxdepth: 2 - - general.averaging - general.convolution - general.deconvolution - general.descriptive - general.forward - general.optimization - general.segmentation - general.uncertainty diff --git a/docs/source/reference/general.segmentation.rst b/docs/source/reference/general.segmentation.rst deleted file mode 100755 index 3d73eb0..0000000 --- a/docs/source/reference/general.segmentation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Segmentation -============ - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/general.uncertainty.rst b/docs/source/reference/general.uncertainty.rst deleted file mode 100755 index 1d2b54b..0000000 --- a/docs/source/reference/general.uncertainty.rst +++ /dev/null @@ -1,12 +0,0 @@ -Uncertainty -=========== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst deleted file mode 100755 index 293b008..0000000 --- a/docs/source/reference/index.rst +++ /dev/null @@ -1,22 +0,0 @@ -######### -Reference -######### - -This reference manual details all functions included in ``osipi``, describing what they are and what they do. Documentation of individual functions contains self-contained example code that demonstrates basic usage of the function. - -The ``osipi`` package currently only includes methods for the dynamic contrast (DC) approach to perfusion MRI (DC-MRI, a unifying term for the separate fields DCE-MRI and DSC-MRI). In particular arterial spin labelling (ASL) solutions are not currently included, but may be added in the future. - -This reference guide, like the ``osipi`` package itself, adheres closely to the structure and language of the `OSIPI Lexicon `_. - - -.. warning:: - - ``osipi`` is in development and this reference guide currently contains mainly empty placeholder entries. - -.. toctree:: - :maxdepth: 2 - - alphabetical - models - processes - general diff --git a/docs/source/reference/models.concentration.aif.rst b/docs/source/reference/models.concentration.aif.rst deleted file mode 100755 index 495ab2a..0000000 --- a/docs/source/reference/models.concentration.aif.rst +++ /dev/null @@ -1,16 +0,0 @@ -AIF models -^^^^^^^^^^ - -.. currentmodule:: osipi - - -Population AIFs ---------------- - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - aif_parker - aif_georgiou - aif_weinmann diff --git a/docs/source/reference/models.concentration.rst b/docs/source/reference/models.concentration.rst deleted file mode 100755 index 3f8fc54..0000000 --- a/docs/source/reference/models.concentration.rst +++ /dev/null @@ -1,9 +0,0 @@ -Concentrations -============== - - -.. toctree:: - :maxdepth: 2 - - models.concentration.aif - models.concentration.tissue diff --git a/docs/source/reference/models.concentration.tissue.rst b/docs/source/reference/models.concentration.tissue.rst deleted file mode 100755 index 6e20d6d..0000000 --- a/docs/source/reference/models.concentration.tissue.rst +++ /dev/null @@ -1,15 +0,0 @@ -Tissue models -^^^^^^^^^^^^^ - -.. currentmodule:: osipi - - -Tofts model ------------ - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - tofts - extended_tofts diff --git a/docs/source/reference/models.descriptive.rst b/docs/source/reference/models.descriptive.rst deleted file mode 100755 index 5f07373..0000000 --- a/docs/source/reference/models.descriptive.rst +++ /dev/null @@ -1,12 +0,0 @@ -Descriptive models -================== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/models.empproperties.rst b/docs/source/reference/models.empproperties.rst deleted file mode 100755 index 62ad397..0000000 --- a/docs/source/reference/models.empproperties.rst +++ /dev/null @@ -1,12 +0,0 @@ -Models for electromagnetic tissue properties -============================================ - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/models.identity.rst b/docs/source/reference/models.identity.rst deleted file mode 100755 index a7dfd62..0000000 --- a/docs/source/reference/models.identity.rst +++ /dev/null @@ -1,13 +0,0 @@ -Perfusion identities -==================== - -.. currentmodule:: osipi - - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/models.leakage.rst b/docs/source/reference/models.leakage.rst deleted file mode 100755 index 868549f..0000000 --- a/docs/source/reference/models.leakage.rst +++ /dev/null @@ -1,12 +0,0 @@ -Leakage correction models -========================= - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/models.rst b/docs/source/reference/models.rst deleted file mode 100755 index bcfa068..0000000 --- a/docs/source/reference/models.rst +++ /dev/null @@ -1,13 +0,0 @@ -****** -Models -****** - -.. toctree:: - :maxdepth: 2 - - models.concentration - models.descriptive - models.empproperties - models.identity - models.leakage - models.signal diff --git a/docs/source/reference/models.signal.rst b/docs/source/reference/models.signal.rst deleted file mode 100755 index 3c85ac3..0000000 --- a/docs/source/reference/models.signal.rst +++ /dev/null @@ -1,15 +0,0 @@ -Signal models -============= - -.. currentmodule:: osipi - - -Magnitude models: DCE - R1 in the fast water exchange limit ------------------------------------------------------------ - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - signal_linear - signal_SPGR diff --git a/docs/source/reference/processes.R1.rst b/docs/source/reference/processes.R1.rst deleted file mode 100755 index 5415ebc..0000000 --- a/docs/source/reference/processes.R1.rst +++ /dev/null @@ -1,14 +0,0 @@ -R1 measurement -============== - -.. currentmodule:: osipi - - -Signal to R1 ---------------- - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - S_to_R1_SPGR diff --git a/docs/source/reference/processes.aif.rst b/docs/source/reference/processes.aif.rst deleted file mode 100755 index ab72f30..0000000 --- a/docs/source/reference/processes.aif.rst +++ /dev/null @@ -1,12 +0,0 @@ -AIF -=== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/processes.baseline.rst b/docs/source/reference/processes.baseline.rst deleted file mode 100755 index 0ce0470..0000000 --- a/docs/source/reference/processes.baseline.rst +++ /dev/null @@ -1,12 +0,0 @@ -Baseline -======== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/processes.bat.rst b/docs/source/reference/processes.bat.rst deleted file mode 100755 index 758e670..0000000 --- a/docs/source/reference/processes.bat.rst +++ /dev/null @@ -1,12 +0,0 @@ -Bolus Arrival Time -================== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/processes.calibration.rst b/docs/source/reference/processes.calibration.rst deleted file mode 100755 index 3c49b98..0000000 --- a/docs/source/reference/processes.calibration.rst +++ /dev/null @@ -1,12 +0,0 @@ -Calibration -=========== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/processes.concentration.rst b/docs/source/reference/processes.concentration.rst deleted file mode 100755 index e06ba21..0000000 --- a/docs/source/reference/processes.concentration.rst +++ /dev/null @@ -1,22 +0,0 @@ -Concentration -============= - -.. currentmodule:: osipi - -Signal to Concentration ------------------------ - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - S_to_C_via_R1_SPGR - -R1 to Concentration -------------------- - -.. autosummary:: - :toctree: ../generated/api/ - :template: autosummary.rst - - R1_to_C_linear_relaxivity diff --git a/docs/source/reference/processes.leakage.rst b/docs/source/reference/processes.leakage.rst deleted file mode 100755 index 5fa2240..0000000 --- a/docs/source/reference/processes.leakage.rst +++ /dev/null @@ -1,12 +0,0 @@ -Leakage -======= - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/processes.parameters.rst b/docs/source/reference/processes.parameters.rst deleted file mode 100755 index 231adcc..0000000 --- a/docs/source/reference/processes.parameters.rst +++ /dev/null @@ -1,12 +0,0 @@ -Parameters -========== - -.. currentmodule:: osipi - -.. note:: - - This is a placeholder page. There is no relevant functionality in ``osipi`` yet. - - Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to.. - - See :ref:`developer-guide` for guidance on how to contribute. diff --git a/docs/source/reference/processes.rst b/docs/source/reference/processes.rst deleted file mode 100755 index a12e51e..0000000 --- a/docs/source/reference/processes.rst +++ /dev/null @@ -1,15 +0,0 @@ -********* -Processes -********* - -.. toctree:: - :maxdepth: 2 - - processes.aif - processes.baseline - processes.bat - processes.calibration - processes.concentration - processes.leakage - processes.parameters - processes.R1 diff --git a/docs/source/user_guide/forward/forward.rst b/docs/source/user_guide/forward/forward.rst deleted file mode 100755 index efd4c8f..0000000 --- a/docs/source/user_guide/forward/forward.rst +++ /dev/null @@ -1,48 +0,0 @@ - -Generating an AIF -^^^^^^^^^^^^^^^^^ - -Generate an AIF and plot it: - -.. code-block:: python - - import numpy as np - import matplotlib.pyplot as plt - import osipi - - t = np.arange(0, 6*60, 1) - ca = osipi.aif_parker(t) - plt.plot(t, ca) - plt.show() - - -Generating a tissue concentration -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Generate tissue concentration and plot it: - -.. code-block:: python - - import numpy as np - import matplotlib.pyplot as plt - import osipi - - t = np.arange(0, 6*60, 1) - ca = osipi.aif_parker(t) - Ktrans = 0.6 - ve = 0.2 - ct = osipi.tofts(t, ca, Ktrans=Ktrans/60, ve=ve) - plt.plot(t, ct) - plt.show() - - -Generating an MRI signal -^^^^^^^^^^^^^^^^^^^^^^^^ - -Coming soon.. - - -Adding measurement error -^^^^^^^^^^^^^^^^^^^^^^^^ - -Coming soon.. diff --git a/docs/source/user_guide/forward/index.rst b/docs/source/user_guide/forward/index.rst deleted file mode 100755 index c16e04f..0000000 --- a/docs/source/user_guide/forward/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -*************** -Simulating data -*************** - -.. toctree:: - :maxdepth: 2 - - forward diff --git a/docs/source/user_guide/index.rst b/docs/source/user_guide/index.rst deleted file mode 100755 index b3a9ebd..0000000 --- a/docs/source/user_guide/index.rst +++ /dev/null @@ -1,15 +0,0 @@ -########## -User guide -########## - -.. note:: - - This page is currently under construction. Please come back later, or better yet, contribute! See :ref:`developer-guide` for guidance on how to contribute documentation. - - -.. toctree:: - :maxdepth: 2 - - installation - forward/index - inverse/index diff --git a/docs/source/user_guide/installation.rst b/docs/source/user_guide/installation.rst deleted file mode 100755 index d6a9fb1..0000000 --- a/docs/source/user_guide/installation.rst +++ /dev/null @@ -1,9 +0,0 @@ -**************** -Installing osipi -**************** - -``osipi`` can be installed using pip: - -.. code-block:: console - - pip install osipi diff --git a/docs/source/user_guide/inverse/index.rst b/docs/source/user_guide/inverse/index.rst deleted file mode 100755 index 8a48688..0000000 --- a/docs/source/user_guide/inverse/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -************ -Fitting data -************ - -.. toctree:: - :maxdepth: 2 - - inverse diff --git a/docs/source/user_guide/inverse/inverse.rst b/docs/source/user_guide/inverse/inverse.rst deleted file mode 100755 index b4e9ba9..0000000 --- a/docs/source/user_guide/inverse/inverse.rst +++ /dev/null @@ -1,51 +0,0 @@ - -Signal to relaxation time -^^^^^^^^^^^^^^^^^^^^^^^^^ - -Convert a series of T1-weighted signal values to the corresponding R1 values. - -.. code-block:: python - - import numpy as np - import matplotlib.pyplot as plt - import osipi - - S = np.array([7, 9, 6, 10, 9, 6, 9, 10, 9, 9, 9, 12, 8, 10, 12, 15, 53, 70, 71, 70, 63, 58, 54, 50, 53, 48, 52, 49, 42], dtype=np.float64) - S_baseline = np.float64(S[0]) # use first point for baseline signal - R10 = np.float64(1/1.4) - TR = np.float64(.002) - a = np.float64(13) - R1 = osipi.S_to_R1_SPGR(S, S_baseline, R10, TR, a) - plt.plot(R1) - plt.ylabel('R1 (/s)') - plt.show() - -Relaxation time to concentration -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Convert a series of R1 values to the corresponding indicator concentrations. - -.. code-block:: python - - import numpy as np - import matplotlib.pyplot as plt - import osipi - - R1 = np.array([1, 2, 3, 4, 5, 6], dtype=np.float64) - R10 = np.float64(1) - r1 = np.float64(5) - - C = osipi.R1_to_C_linear_relaxivity(R1, R10, r1) - plt.plot(C) - plt.ylabel('C (mM)') - plt.show() - -Concentration to tissue parameters -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Coming soon.. - -All in one go: signal to tissue parameters -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Coming soon.. diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css new file mode 100644 index 0000000..9409af0 --- /dev/null +++ b/docs/stylesheets/extra.css @@ -0,0 +1,36 @@ +.md-header__button.md-logo img{ +height: 50px; + +} + + +.model-table { + display: table; + width: 100%; + border-collapse: collapse; +} + +.model-row { + display: table-row; +} + +.model-name, .model-description { + display: table-cell; + padding: 10px; + vertical-align: top; +} + +.model-name { + width: 20%; + font-weight: bold; +} + +.model-description { + width: 80%; +} + +hr { + margin: 0; + border: 0; + border-top: 1px solid #ccc; +} diff --git a/docs/user-guide/gen_aif.md b/docs/user-guide/gen_aif.md new file mode 100644 index 0000000..8143615 --- /dev/null +++ b/docs/user-guide/gen_aif.md @@ -0,0 +1,37 @@ + + +## Generate an AIF and plot it: +``` py +import numpy as np +import matplotlib.pyplot as plt +import osipi + +t = np.arange(0, 6*60, 1) +ca = osipi.aif_parker(t) +plt.plot(t, ca) +plt.show() +``` + +## Generating a tissue concentration + +``` py +import numpy as np +import matplotlib.pyplot as plt +import osipi + +t = np.arange(0, 6*60, 1) +ca = osipi.aif_parker(t) +Ktrans = 0.6 +ve = 0.2 +ct = osipi.tofts(t, ca, Ktrans=Ktrans/60, ve=ve) +plt.plot(t, ct) +plt.show() +``` + +## Generating an MRI signal +!!! note "Coming Soon" + This section is under development and will be available soon. + +## Adding measurement error +!!! note "Coming Soon" + This section is under development and will be available soon. diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md new file mode 100644 index 0000000..e21bfa6 --- /dev/null +++ b/docs/user-guide/index.md @@ -0,0 +1,17 @@ +# User Guide + +Welcome to the User Guide section. + +## Contents + +1. [Installing osipi](install.md) +2. [Simulating data](simulate.md) + - [Generating an AIF](simulate.md) + - [Generating a tissue concentration](simulate.md) + - [Generating an MRI signal](simulate.md) + - [Adding measurement error](simulate.md) +3. [Fitting data](simulate.md) + - [Signal to relaxation time](simulate.md) + - [Relaxation time to concentration](simulate.md) + - [Concentration to tissue parameters](simulate.md) + - [All in one go: signal to tissue parameters](simulate.md) diff --git a/docs/user-guide/install.md b/docs/user-guide/install.md new file mode 100644 index 0000000..6ee1bd8 --- /dev/null +++ b/docs/user-guide/install.md @@ -0,0 +1,13 @@ +# Installing osipi + +## Step 1: Prerequisites + +Ensure you have Python installed. You can download it from the [official Python website](https://www.python.org/downloads/). + +## Step 2: Install Using pip + +To install the package using `pip`, open your terminal and run the following command: + +``` +pip install osipi +``` diff --git a/docs/user-guide/simulate.md b/docs/user-guide/simulate.md new file mode 100644 index 0000000..b4b62bf --- /dev/null +++ b/docs/user-guide/simulate.md @@ -0,0 +1,5 @@ + +- [Generating an AIF](gen_aif.md#generating-an-aif) +- [Generating a Tissue Concentration](gen_aif.md#generating-a-tissue-concentration) +- [Generating an MRI Signal](gen_aif.md#generating-an-mri-signal) +- [Adding Measurement Error](gen_aif.md#adding-measurement-error) diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..8c1e0b6 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,109 @@ +site_name: '' +repo_url: https://github.com/OSIPI/pypi +theme: + name: material + logo: img/osipi.png + icon: + repo: fontawesome/brands/github + features: + - header.autohide + - navigation.tabs + - navigation.tabs.sticky + - navigation.instant + - navigation.instant.progress + - navigation.sections + - navigation.footer + - navigation.indexes + - toc.integrate + - navigation.top + - search.suggest + - search.highlight + - search.share + - content.tabs.link + - content.code.annotation + - content.code.copy + - content.code.select + - tables + language: en + palette: + - scheme: default + primary: teal + accent: purple + toggle: + icon: material/toggle-switch + name: Switch to dark mode + - scheme: slate + toggle: + icon: material/toggle-switch + name: Switch to dark mode + primary: teal + accent: lime + +plugins: + - mkdocstrings: + default_handler: python + - gallery: + examples_dirs: docs/examples + gallery_dirs: docs/generated/gallery + +extra_css: + - stylesheets/extra.css + +nav: + - Home: index.md + - User Guide: + - Overview: user-guide/index.md + - Installation: user-guide/install.md + - Simulating data: + - Overview: user-guide/simulate.md + - Simulate: user-guide/gen_aif.md + + - About: about/index.md + - Developer Guide: contribution/index.md + - References: + - references/index.md + - Index: + - references/models/index.md + - AIF models: + - references/models/aif_models/index.md + - osipi.aif_parker: references/models/aif_models/aif_parker.md + - osipi.aif_georgiou: references/models/aif_models/aif_georgiou.md + - osipi.aif_weinmann: references/models/aif_models/aif_weinmann.md + - Tissue models : + - references/models/tissue_models/index.md + - osipi.tofts: references/models/tissue_models/tofts.md + - osipi.extended_tofts: references/models/tissue_models/extended_tofts.md + + - Examples: generated/gallery + + +markdown_extensions: + - admonition + - codehilite + - footnotes + - meta + - toc: + permalink: true + - tables + - pymdownx.arithmatex + - pymdownx.betterem: + smart_enable: all + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.caret + - pymdownx.critic + - pymdownx.details + - pymdownx.inlinehilite + - pymdownx.magiclink + - pymdownx.mark + - pymdownx.smartsymbols + - pymdownx.superfences + - pymdownx.details + - pymdownx.tasklist: + custom_checkbox: true + - pymdownx.tilde + - pymdownx.tabbed: + alternate_style: true + - attr_list diff --git a/poetry.lock b/poetry.lock index 597bcc6..3a4faf0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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