diff --git a/.all-contributorsrc b/.all-contributorsrc index 764196fae..4ac2afe53 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -12,10 +12,13 @@ "profile": "https://github.com/sebastientourbier", "contributions": [ "design", - "test", "code", + "infra", + "test", + "bug", "example", "doc", + "ideas", "review" ] }, @@ -25,10 +28,13 @@ "avatar_url": "https://avatars2.githubusercontent.com/u/19345763?v=4", "profile": "https://github.com/pdedumast", "contributions": [ + "design", "example", "test", "code", - "doc" + "doc", + "ideas", + "review" ] }, { @@ -40,16 +46,23 @@ "example", "test", "code", - "doc" + "doc", + "ideas" ] }, { - "login": "meribach", - "name": "Meritxell Bach", - "avatar_url": "https://avatars3.githubusercontent.com/u/2786897?v=4", - "profile": "https://github.com/meribach", + "login": "t-sanchez", + "name": "Thomas Sanchez", + "avatar_url": "https://avatars.githubusercontent.com/u/14288440?v=4", + "profile": "http://t-sanchez.github.io", "contributions": [ - "fundingFinding" + "bug", + "code", + "doc", + "example", + "ideas", + "infra", + "review" ] }, { @@ -72,6 +85,15 @@ "data", "fundingFinding" ] + }, + { + "login": "meribach", + "name": "Meritxell Bach", + "avatar_url": "https://avatars3.githubusercontent.com/u/2786897?v=4", + "profile": "https://github.com/meribach", + "contributions": [ + "fundingFinding" + ] } ], "contributorsPerLine": 7, @@ -79,5 +101,6 @@ "projectOwner": "Medical-Image-Analysis-Laboratory", "repoType": "github", "repoHost": "https://github.com", - "skipCi": true + "skipCi": true, + "commitConvention": "angular" } diff --git a/.circleci/config.yml b/.circleci/config.yml index 60686e724..780ad7f42 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -807,14 +807,14 @@ workflows: tags: only: /^v.*/ -# - deploy-singularity-latest: -# requires: -# - build-singularity -# # - build_docs -# - test-singularity -# - codacy-coverage-report -# filters: -# # ignore any commit on any branch by default -# branches: -# only: master + - deploy-singularity-latest: + requires: + - build-singularity + # - build_docs + - test-singularity + - codacy-coverage-report + filters: + # ignore any commit on any branch by default + branches: + only: master diff --git a/.circleci/test-01_outputs.txt b/.circleci/test-01_outputs.txt index 8af70f586..003349574 100644 --- a/.circleci/test-01_outputs.txt +++ b/.circleci/test-01_outputs.txt @@ -11,247 +11,247 @@ manual_masks/sub-01/anat/sub-01_run-5_T2w_desc-brain_mask.json manual_masks/sub-01/anat/sub-01_run-5_T2w_desc-brain_mask.nii.gz manual_masks/sub-01/anat/sub-01_run-6_T2w_desc-brain_mask.json manual_masks/sub-01/anat/sub-01_run-6_T2w_desc-brain_mask.nii.gz -nipype-1.8.3/dataset_description.json -nipype-1.8.3/sub-01/rec-1/pypeline.log -nipype-1.8.3/sub-01/rec-1/srr_pipeline/d3.js -nipype-1.8.3/sub-01/rec-1/srr_pipeline/graph1.json -nipype-1.8.3/sub-01/rec-1/srr_pipeline/graph.dot -nipype-1.8.3/sub-01/rec-1/srr_pipeline/graph.json 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pymialsrtk-2.1.0/sub-01/anat/sub-01_rec-SDI_id-1_T2w.nii.gz pymialsrtk-2.1.0/sub-01/anat/sub-01_rec-SR_id-1_desc-motion_stats.tsv @@ -275,6 +275,6 @@ pymialsrtk-2.1.0/sub-01/figures/sub-01_rec-SR_id-1_desc-processing_graph.png pymialsrtk-2.1.0/sub-01/figures/sub-01_rec-SR_id-1_T2w.png pymialsrtk-2.1.0/sub-01/logs/sub-01_rec-SR_id-1_log.txt pymialsrtk-2.1.0/sub-01/report/sub-01_rec-SR_id-1_desc-report_T2w.html -pymialsrtk-2.1.0/sub-01/xfm/sub-01_run-1_T2w_uni_bcorr_histnorm_transform_3V.txt -pymialsrtk-2.1.0/sub-01/xfm/sub-01_run-3_T2w_uni_bcorr_histnorm_transform_3V.txt -pymialsrtk-2.1.0/sub-01/xfm/sub-01_run-6_T2w_uni_bcorr_histnorm_transform_3V.txt +pymialsrtk-2.1.0/sub-01/xfm/sub-01_run-1_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt +pymialsrtk-2.1.0/sub-01/xfm/sub-01_run-3_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt +pymialsrtk-2.1.0/sub-01/xfm/sub-01_run-6_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt diff --git a/.zenodo.json b/.zenodo.json index 1a95b3702..feb765949 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -10,31 +10,40 @@ "BIDS", "bids-apps" ], - "publication_date": "2020-12-24", "creators": [ { "name": "Tourbier, Sebastien", - "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland", + "affiliation": "Department of Clinical Neuroscience, Lausanne University Hospital (CHUV), Switzerland", "orcid": "0000-0002-4441-899X" }, { "name": "De Dumast, Priscille", - "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland", + "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland", "orcid": "0000-0003-0359-9365" }, { "name": "Kebiri, Hamza", - "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland", + "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland", "orcid": "0000-0001-7592-3166" }, + { + "name": "Sanchez, Thomas", + "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland", + "orcid": "0000-0003-3668-5155" + }, + { + "name": "Lajous, Helene", + "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland", + "orcid": "0000-0001-7729-6274" + }, { "name": "Hagmann, Patric", - "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland", + "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland", "orcid": "0000-0002-2854-6561" }, { "name": "Bach Cuadra, Meritxell", - "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland", + "affiliation": "Department of Diagnostic and Interventional Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Switzerland; Center for Biomedical Imaging (CIBM), Switzerland", "orcid": "0000-0003-2730-4285" } ], diff --git a/Dockerfile b/Dockerfile index a737f32cb..3ae07b40e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -68,8 +68,12 @@ WORKDIR /opt/mialsuperresolutiontoolkit/build # You can increase the number of cores used by make ("make -jN") # to speed up local build. However, make sure that it is # set back to make -j2 before pushing any change to GitHub. -RUN cmake -D CMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=/usr/local -D USE_OMP:BOOL=ON ../src \ - && make -j6 && make install +RUN cmake \ + -D CMAKE_BUILD_TYPE=Release \ + -D CMAKE_INSTALL_PREFIX=/usr/local \ + -D USE_OMP:BOOL=ON ../src && \ + make -j6 && \ + make install ############################################################## # Python cache setup and creation of conda environment diff --git a/README.md b/README.md index 9a2974052..2379f4d36 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # ![MIALSRTK logo](https://raw.githubusercontent.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/dev-pgd-hk/documentation/images/mialsrtk-logo.png) --- -Copyright © 2016-2020 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland This software is distributed under the open-source BSD 3-Clause License. See [LICENSE](LICENSE.txt) file for details. @@ -47,14 +47,16 @@ All these design considerations allow us not only to (1) represent the entire pr $ mialsuperresolutiontoolkit_[docker|singularity] -h usage: mialsuperresolutiontoolkit_[docker|singularity] [-h] + [--run_type {sr,preprocessing}] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--param_file PARAM_FILE] [--openmp_nb_of_cores OPENMP_NB_OF_CORES] [--nipype_nb_of_cores NIPYPE_NB_OF_CORES] [--memory MEMORY] [--masks_derivatives_dir MASKS_DERIVATIVES_DIR] - [-v] - [--codecarbon_output_dir CODECARBON_OUTPUT_DIR] + [--labels_derivatives_dir LABELS_DERIVATIVES_DIR] + [--all_outputs] [-v] [--verbose] + [--track_carbon_footprint] bids_dir output_dir {participant} Argument parser of the MIALSRTK BIDS App Python wrapper @@ -71,6 +73,10 @@ All these design considerations allow us not only to (1) represent the entire pr optional arguments: -h, --help show this help message and exit + --run_type {sr,preprocessing} + Type of pipeline that is run. Can choose between + running the super-resolution pipeline (`sr`) or only + preprocessing (`preprocessing`). --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...] The label(s) of the participant(s) that should be analyzed. The label corresponds to @@ -101,12 +107,18 @@ All these design considerations allow us not only to (1) represent the entire pr --masks_derivatives_dir MASKS_DERIVATIVES_DIR Use manual brain masks found in ``//`` directory - --codecarbon_output_dir CODECARBON_OUTPUT_DIR - Directory path in which `codecarbon` saves a CSV file - called `emissions.csv` reporting carbon footprint - details of the overall run (Defaults to user’s home - directory) + --labels_derivatives_dir LABELS_DERIVATIVES_DIR + Use low-resolution labelmaps found in + ``//`` directory. + --all_outputs Whether or not all outputs should be kept(e.g. + preprocessed LR images) -v, --version show program's version number and exit + --verbose Verbose mode + --track_carbon_footprint + Track carbon footprint with `codecarbon + `_ and save results in a CSV + file called ``emissions.csv`` in the + ``/code`` directory. ## Credits @@ -114,14 +126,17 @@ All these design considerations allow us not only to (1) represent the entire pr - - - - - - - - + + + + + + + + + + +

Sébastien Tourbier
🎨 ⚠️ 💻 💡 📖 👀
Priscille de Dumast
💡 ⚠️ 💻 📖
hamzake
💡 ⚠️ 💻 📖
Hélène Lajous
🐛 ⚠️
Patric Hagmann
🔣 🔍
Meritxell Bach
🔍
Sébastien Tourbier
Sébastien Tourbier
🎨 💻 🚇 ⚠️ 🐛 💡 📖 🤔 👀		Priscille de Dumast
Priscille de Dumast
🎨 💡 ⚠️ 💻 📖 🤔 👀		hamzake
hamzake
💡 ⚠️ 💻 📖 🤔		Thomas Sanchez
Thomas Sanchez
🐛 💻 📖 💡 🤔 🚇 👀		Hélène Lajous
Hélène Lajous
🐛 ⚠️ 👀		Patric Hagmann
Patric Hagmann
🔣 🔍		Meritxell Bach
Meritxell Bach
🔍
diff --git a/docker/bidsapp/environment.yml b/docker/bidsapp/environment.yml index 222d5a622..7aa225e49 100644 --- a/docker/bidsapp/environment.yml +++ b/docker/bidsapp/environment.yml @@ -10,14 +10,14 @@ dependencies: - python=3.7.10 - pip=21.0.1 - pandas=1.1.5 -- nipype=1.8.3 -- nilearn=0.8.1 +- nipype=1.8.4 +- nilearn=0.8.0 - pydotplus=2.0.2 - pandoc=2.14.2 - seaborn=0.11.2 - matplotlib=3.4 - tensorflow==1.13.1 -- scikit-learn=1.0.1 +- scikit-learn=0.21.3 - scikit-image=0.16.2 - ants=2.2.0 diff --git a/docker/bidsapp/run.py b/docker/bidsapp/run.py index 3289403a8..f481e4a6b 100644 --- a/docker/bidsapp/run.py +++ b/docker/bidsapp/run.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. diff --git a/documentation/api_pipelines.rst b/documentation/api_pipelines.rst index 67512371e..fdabcb874 100644 --- a/documentation/api_pipelines.rst +++ b/documentation/api_pipelines.rst @@ -4,6 +4,14 @@ Pipelines module ****************** +.. automodule:: pymialsrtk.pipelines.anatomical.abstract + :members: + :show-inheritance: + +.. automodule:: pymialsrtk.pipelines.anatomical.preprocessing + :members: + :show-inheritance: + .. automodule:: pymialsrtk.pipelines.anatomical.srr :members: :show-inheritance: diff --git a/documentation/api_workflows.rst b/documentation/api_workflows.rst new file mode 100644 index 000000000..a8680a887 --- /dev/null +++ b/documentation/api_workflows.rst @@ -0,0 +1,33 @@ +.. _apidoc_workflows: + +****************** +Workflows module +****************** + +.. automodule:: pymialsrtk.workflows.input_stage + :members: + :show-inheritance: + +.. automodule:: pymialsrtk.workflows.preproc_stage + :members: + :show-inheritance: + +.. automodule:: pymialsrtk.workflows.registration_stage + :members: + :show-inheritance: + +.. automodule:: pymialsrtk.workflows.recon_stage + :members: + :show-inheritance: + +.. automodule:: pymialsrtk.workflows.recon_labelmap_stage + :members: + :show-inheritance: + +.. automodule:: pymialsrtk.workflows.srr_assessment_stage + :members: + :show-inheritance: + +.. automodule:: pymialsrtk.workflows.output_stage + :members: + :show-inheritance: diff --git a/documentation/citing.rst b/documentation/citing.rst index 2927da4a2..5d7e27f77 100644 --- a/documentation/citing.rst +++ b/documentation/citing.rst @@ -7,7 +7,7 @@ Citing .. important:: * If your are using the MIALSRTK BIDS App, a manuscript is in preparation, but for now, please acknowledge this software with the following three entries: - 1. Tourbier S, De Dumast P., Kebiri H., Hagmann P., Bach Cuadra M. (2020, November 25). Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit: MIAL Super-Resolution Toolkit (Version v2.0.0). Zenodo. http://doi.org/10.5281/zenodo.4290209 + 1. Tourbier S, De Dumast P., Kebiri H., Sanchez T., Lajous H., Hagmann P., Bach Cuadra M. (2023, January 31). Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit: MIAL Super-Resolution Toolkit (Version v2.1.0). Zenodo. http://doi.org/10.5281/zenodo.4290209 2. Tourbier S, Bresson X, Hagmann P, Meuli R, Bach Cuadra M, *An efficient total variation algorithm for super-resolution in fetal brain MRI with adaptive regularization*, Neuroimage 118 (2015) 584-597. doi:10.1016/j.neuroimage.2015.06.018 diff --git a/documentation/conf.py b/documentation/conf.py index 95342097a..5befe6c36 100644 --- a/documentation/conf.py +++ b/documentation/conf.py @@ -15,7 +15,7 @@ import os import sys -sys.path.append('../') # noqa: 402 +sys.path.append("../") # noqa: 402 # sys.path.insert(0,"'../pymialsrtk/'") from pymialsrtk.info import __minor_version__ @@ -36,7 +36,7 @@ def visit_document(self, node): # 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('../pymialsrtk')) +sys.path.insert(0, os.path.abspath("../pymialsrtk")) # -- General configuration ----------------------------------------------------- @@ -45,34 +45,37 @@ def visit_document(self, node): # 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.autosectionlabel', - 'sphinx.ext.autodoc', - 'sphinx.ext.mathjax', - 'sphinx.ext.viewcode', - 'sphinxarg.ext', - 'sphinx.ext.inheritance_diagram', - 'sphinxcontrib.apidoc', - 'nbsphinx', - 'nipype.sphinxext.plot_workflow', - 'nipype.sphinxext.apidoc', - 'pymialsrtk.sphinxext.documenter', - 'sphinxemoji.sphinxemoji', - ] +extensions = [ + "sphinx.ext.autosectionlabel", + "sphinx.ext.autodoc", + "sphinx.ext.mathjax", + "sphinx.ext.viewcode", + "sphinxarg.ext", + "sphinx.ext.inheritance_diagram", + "sphinxcontrib.apidoc", + "nbsphinx", + "nipype.sphinxext.plot_workflow", + "nipype.sphinxext.apidoc", + "pymialsrtk.sphinxext.documenter", + "sphinxemoji.sphinxemoji", +] # autodoc_default_options = { # 'autosummary': True, # } autodoc_mock_imports = [ - 'cv2', - 'codecarbon', - 'skimage', - 'matplotlib', - 'seaborn', - 'pandas', - 'nilearn', - 'tflearn', - 'tensorflow' + "cv2", + "codecarbon", + "skimage", + "matplotlib", + "nsol", + "seaborn", + "SimpleITK", + "pandas", + "nilearn", + "tflearn", + "tensorflow", ] # Accept custom section names to be parsed for numpy-style docstrings @@ -93,8 +96,8 @@ def visit_document(self, node): if on_rtd: extensions.append("readthedocs_ext.readthedocs") -apidoc_module_dir = '../pymialsrtk' -apidoc_output_dir = 'api/generated' +apidoc_module_dir = "../pymialsrtk" +apidoc_output_dir = "api/generated" # apidoc_excluded_paths = ['tests'] apidoc_separate_modules = True @@ -102,27 +105,31 @@ def visit_document(self, node): nbsphinx_allow_errors = True # Consistent emoticon style -sphinxemoji_style = 'twemoji' +sphinxemoji_style = "twemoji" # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # Use Markdown and reStructuredText in the same Sphinx project source_parsers = { - '.md': CustomCommonMarkParser, + ".md": CustomCommonMarkParser, } # The suffix of source filenames. -source_suffix = ['.rst', '.md'] +source_suffix = [".rst", ".md"] # The encoding of source files. # source_encoding = 'utf-8-sig' # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = u'Medical Image Analysis Laboratory Super-Resolution Toolkit' -copyright = u'2016-{}, Medical Image Analysis Laboratory (MIAL) & Contributors'.format(time.strftime("%Y")) +project = "Medical Image Analysis Laboratory Super-Resolution Toolkit" +copyright = ( + "2016-{}, Medical Image Analysis Laboratory (MIAL) & Contributors".format( + time.strftime("%Y") + ) +) # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -137,8 +144,7 @@ def visit_document(self, node): .. |pypirelease| replace:: {} .. |vrelease| replace:: {} """.format( - f'pymialsrtk=={release}', - f'v{release}' + f"pymialsrtk=={release}", f"v{release}" ) # The language for content autogenerated by Sphinx. Refer to documentation @@ -153,8 +159,8 @@ def visit_document(self, node): # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build'] -default_role = 'obj' +exclude_patterns = ["_build"] +default_role = "obj" # The reST default role (used for this markup: `text`) to use for all documents. # default_role = None @@ -171,7 +177,7 @@ def visit_document(self, node): # show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] @@ -183,15 +189,15 @@ def visit_document(self, node): # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'sphinx_rtd_theme' # 'sphinxdoc' +html_theme = "sphinx_rtd_theme" # 'sphinxdoc' # html_theme = 'alabaster'#'sphinxdoc' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. html_theme_options = { - 'logo_only': True, # should be commented if html_theme = 'alabaster' - 'display_version': False + "logo_only": True, # should be commented if html_theme = 'alabaster' + "display_version": False, } # Add any paths that contain custom themes here, relative to this directory. @@ -202,11 +208,11 @@ def visit_document(self, node): # html_title = 'The MIAL Super-Resolution Toolkit' # A shorter title for the navigation bar. Default is the same as html_title. -html_short_title = u'MIALSRTK' +html_short_title = "MIALSRTK" # The name of an image file (relative to this directory) to place at the top # of the sidebar. -html_logo = 'images/mialsrtk-logo.png' +html_logo = "images/mialsrtk-logo.png" # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 @@ -216,11 +222,11 @@ def visit_document(self, node): # 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'] +html_static_path = ["_static"] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -html_last_updated_fmt = '%b %d, %Y' +html_last_updated_fmt = "%b %d, %Y" # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. @@ -260,9 +266,9 @@ def visit_document(self, node): # html_file_suffix = None # Output file base name for HTML help builder. -htmlhelp_basename = 'MIALSRTKdoc' +htmlhelp_basename = "MIALSRTKdoc" -html_context = {'release_date': __release_date__} +html_context = {"release_date": __release_date__} # Activate autosectionlabel plugin autosectionlabel_prefix_document = True @@ -271,48 +277,46 @@ def visit_document(self, node): latex_elements = { # The paper size ('letterpaper' or 'a4paper'). - 'papersize': 'a4paper', - + "papersize": "a4paper", # The font size ('10pt', '11pt' or '12pt'). - 'pointsize': '10pt', - + "pointsize": "10pt", # Additional package # 'extrapackages': r'', - # Font settings -# 'fontpkg': r''' -# \setmainfont{DejaVu Serif} -# \setsansfont{DejaVu Sans} -# \setmonofont{DejaVu Sans Mono} -# ''', - + # 'fontpkg': r''' + # \setmainfont{DejaVu Serif} + # \setsansfont{DejaVu Sans} + # \setmonofont{DejaVu Sans Mono} + # ''', # Additional stuff for the LaTeX preamble. - 'preamble': r''' + "preamble": r""" \usepackage{dejavu} -''', - +""", # Use Fancy chapter - 'fncychap': r'\usepackage[Bjornstrup]{fncychap}', - + "fncychap": r"\usepackage[Bjornstrup]{fncychap}", # Adjust for the large character width of the monospace font, used in code-blocks # 'fvset': r'\\fvset{fontsize=\\footnotesize}', Seems not working! - # Adjust size for long module name in generated index - 'printindex': r''' + "printindex": r""" \tiny\raggedright\printindex -''', +""", } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index', 'MIALSRTK.tex', u'MIALSRTK Documentation', - u'Medical Image Analysis Laboratory and Contributors', 'manual'), + ( + "index", + "MIALSRTK.tex", + "MIALSRTK Documentation", + "Medical Image Analysis Laboratory and Contributors", + "manual", + ), ] # The name of an image file (relative to this directory) to place at the top of # the title page. -latex_logo = 'images/mialsrtk-logo.png' +latex_logo = "images/mialsrtk-logo.png" # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. @@ -324,7 +328,7 @@ def visit_document(self, node): # Specify Latex engine # latex_engine = 'xelatex' -latex_show_urls = 'footnote' +latex_show_urls = "footnote" # If true, show URL addresses after external links. # latex_show_urls = False @@ -341,8 +345,13 @@ def visit_document(self, node): # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - ('index', 'MIALSRTK', u'MIALSRTK Documentation', - [u'Medical Image Analysis Laboratory and Contributors'], 1) + ( + "index", + "MIALSRTK", + "MIALSRTK Documentation", + ["Medical Image Analysis Laboratory and Contributors"], + 1, + ) ] # If true, show URL addresses after external links. @@ -355,10 +364,15 @@ def visit_document(self, node): # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - ('index', 'MIALSRTK', u'MIALSRTK Documentation', - u'Medical Image Analysis Laboratory and Contributors', 'MIALSRTK', - 'Set of C++ image processing and Python workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction.', - 'Science'), + ( + "index", + "MIALSRTK", + "MIALSRTK Documentation", + "Medical Image Analysis Laboratory and Contributors", + "MIALSRTK", + "Set of C++ image processing and Python workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction.", + "Science", + ), ] # Documents to append as an appendix to all manuals. diff --git a/documentation/contributors.rst b/documentation/contributors.rst index 45caeb00f..5d4965757 100644 --- a/documentation/contributors.rst +++ b/documentation/contributors.rst @@ -7,12 +7,13 @@ Contributors .. raw:: html - - - - - - - - -

Sébastien Tourbier
🎨 ⚠️ 💻 💡 📖 👀
Priscille de Dumast
💡 ⚠️ 💻
Hamza Kebiri
💡 ⚠️ 💻
Hélène Lajous
🐛 ⚠️
Patric Hagmann
🔣 🔍
Meritxell Bach
🔍
+ + Sébastien Tourbier
Sébastien Tourbier
🎨 💻 🚇 ⚠️ 🐛 💡 📖 🤔 👀 + Priscille de Dumast
Priscille de Dumast
🎨 💡 ⚠️ 💻 📖 🤔 👀 + hamzake
hamzake
💡 ⚠️ 💻 📖 🤔 + Thomas Sanchez
Thomas Sanchez
🐛 💻 📖 💡 🤔 🚇 👀 + Hélène Lajous
Hélène Lajous
🐛 ⚠️ 👀 + Patric Hagmann
Patric Hagmann
🔣 🔍 + Meritxell Bach
Meritxell Bach
🔍 + + diff --git a/documentation/index.rst b/documentation/index.rst index bb1d1a472..3d312a2c5 100644 --- a/documentation/index.rst +++ b/documentation/index.rst @@ -127,6 +127,7 @@ Contents api_reconstruction api_utils api_pipelines + api_workflows .. _user-usecases: diff --git a/pymialsrtk/bids/utils.py b/pymialsrtk/bids/utils.py index a6a3cb4ec..47a5cc3cc 100644 --- a/pymialsrtk/bids/utils.py +++ b/pymialsrtk/bids/utils.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, +# Copyright © 2016-2023 Medical Image Analysis Laboratory, # University Hospital Center and University of Lausanne (UNIL-CHUV), # Switzerland, and contributors # diff --git a/pymialsrtk/git b/pymialsrtk/git deleted file mode 100644 index e69de29bb..000000000 diff --git a/pymialsrtk/interfaces/postprocess.py b/pymialsrtk/interfaces/postprocess.py index 9d2054ead..9de5926a8 100644 --- a/pymialsrtk/interfaces/postprocess.py +++ b/pymialsrtk/interfaces/postprocess.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. @@ -214,7 +214,7 @@ class MialsrtkN4BiasFieldCorrection(BaseInterface): Example ---------- - >>> from pymialsrtk.interfaces.preprocess import MialsrtkSliceBySliceN4BiasFieldCorrection + >>> from pymialsrtk.interfaces.postprocess import MialsrtkSliceBySliceN4BiasFieldCorrection >>> N4biasFieldCorr = MialsrtkSliceBySliceN4BiasFieldCorrection() >>> N4biasFieldCorr.inputs.input_image = 'sub-01_acq-haste_run-1_SR.nii.gz' >>> N4biasFieldCorr.inputs.input_mask = 'sub-01_acq-haste_run-1_mask.nii.gz' @@ -304,8 +304,7 @@ class FilenamesGenerationOutputSpec(TraitedSpec): class FilenamesGeneration(BaseInterface): - """Generates final filenames from outputs of super-resolution - reconstruction. + """Generates final filenames from outputs of super-resolution reconstruction. Example ---------- @@ -374,6 +373,7 @@ def _run_interface(self, runtime): ) ) + # Transforms if NLM was applied self.m_substitutions.append( ( "_T2w_nlm_uni_bcorr_histnorm_transform_" @@ -385,6 +385,19 @@ def _run_interface(self, runtime): + "mode-image_xfm.txt", ) ) + # Transforms if NLM was not applied + self.m_substitutions.append( + ( + "_T2w_uni_bcorr_histnorm_transform_" + + str(len(self.inputs.stacks_order)) + + "V.txt", + "_id-" + + str(self.inputs.sr_id) + + "_mod-T2w_from-origin_to-SDI_" + + "mode-image_xfm.txt", + ) + ) + for stack in self.inputs.stacks_order: self.m_substitutions.append( ( @@ -675,6 +688,7 @@ class BinarizeImageOutputSpec(TraitedSpec): class BinarizeImage(BaseInterface): """Runs the MIAL SRTK mask image module. + Example ======= >>> from pymialsrtk.interfaces.postprocess import BinarizeImage @@ -750,7 +764,19 @@ class ImageMetricsOutputSpec(TraitedSpec): class ImageMetrics(BaseInterface): - """ """ + """Compute various image metrics on a SR reconstructed image compared to a ground truth. + + Example + ---------- + >>> from pymialsrtk.interfaces.postprocess import ImageMetrics + >>> compute_metrics = ImageMetrics() + >>> compute_metrics.inputs.input_image = 'sub-01_acq-haste_rec-SR_id-1_T2w.nii.gz' + >>> compute_metrics.inputs.input_ref_image = 'sub-01_acq-haste_desc-GT_T2w.nii.gz' + >>> compute_metrics.inputs.input_ref_mask = 'sub-01_acq-haste_desc-GT_T2w_mask.nii.gz' + >>> compute_metrics.inputs.input_TV_parameters = {'in_loop': '10', 'in_deltat': '0.01', 'in_lambda': '2.5', 'in_bregman_loop': '3', 'in_iter': '50', 'in_step_scale': '1', 'in_gamma': '1', 'in_inner_thresh': '1e-05', 'in_outer_thresh': '1e-06'} + >>> concat_metrics.run() # doctest: +SKIP + + """ input_spec = ImageMetricsInputSpec output_spec = ImageMetricsOutputSpec @@ -929,23 +955,31 @@ def _list_outputs(self): class ConcatenateImageMetricsInputSpec(BaseInterfaceInputSpec): - """Class used to represent inputs of - the ConcatenateImageMetrics interface.""" + """Class used to represent inputs of the ConcatenateImageMetrics interface.""" input_metrics = InputMultiPath(File(mandatory=True), desc="") input_metrics_labels = InputMultiPath(File(mandatory=True), desc="") class ConcatenateImageMetricsOutputSpec(TraitedSpec): - """Class used to represent outputs of - the ConcatenateImageMetrics interface.""" + """Class used to represent outputs of the ConcatenateImageMetrics interface.""" output_csv = File(desc="") output_csv_labels = File(desc="") class ConcatenateImageMetrics(BaseInterface): - """ConcatenateImageMetrics""" + """Concatenate metrics CSV files with the metrics computed on each labelmap. + + Example + ---------- + >>> from pymialsrtk.interfaces.postprocess import ConcatenateImageMetrics + >>> concat_metrics = ConcatenateImageMetrics() + >>> concat_metrics.inputs.input_metrics = ['sub-01_acq-haste_run-1_paramset_1_metrics.csv', 'sub-01_acq-haste_run-1_paramset2_metrics.csv'] + concat_metrics.inputs.input_metrics_labels = ['sub-01_acq-haste_run-1_paramset_1_metrics_labels.csv', 'sub-01_acq-haste_run-1_paramset2_metrics_labels.csv'] + >>> concat_metrics.run() # doctest: +SKIP + + """ input_spec = ConcatenateImageMetricsInputSpec output_spec = ConcatenateImageMetricsOutputSpec @@ -1007,7 +1041,16 @@ class MergeMajorityVoteOutputSpec(TraitedSpec): class MergeMajorityVote(BaseInterface): - """Perform majority voting to merge a list of label-wise labelmaps.""" + """Perform majority voting to merge a list of label-wise labelmaps. + + Example + ---------- + >>> from pymialsrtk.interfaces.postprocess import MergeMajorityVote + >>> merge_labels = MergeMajorityVote() + >>> merge_labels.inputs.input_images = ['sub-01_acq-haste_run-1_labels_1.nii.gz', 'sub-01_acq-haste_run-1_labels_2.nii.gz', 'sub-01_acq-haste_run-1_labels_3.nii.gz'] + >>> merge_labels.run() # doctest: +SKIP + + """ input_spec = MergeMajorityVoteInputSpec output_spec = MergeMajorityVoteOutputSpec @@ -1052,8 +1095,7 @@ def _list_outputs(self): class ReportGenerationInputSpec(BaseInterfaceInputSpec): - """Class used to represent inputs of - the ReportGeneration interface.""" + """Class used to represent inputs of the ReportGeneration interface.""" subject = traits.Str( mandatory=True, @@ -1128,18 +1170,46 @@ class ReportGenerationInputSpec(BaseInterfaceInputSpec): class ReportGenerationOutputSpec(TraitedSpec): - """Class used to represent outputs of - the ReportGeneration interface.""" + """Class used to represent outputs of the ReportGeneration interface.""" report_html = File(desc="") class ReportGeneration(BaseInterface): - """Generate a report summarizing the outputs - of mialsrtk. This comprises + """Generate a report summarizing the outputs of mialsrtk. + + This comprises: - Details of which parameters were run. - A visualization of the SR-reconstructed image - A visualization of the computational graph. + + Example + ---------- + >>> from pymialsrtk.interfaces.postprocess import ReportGeneration + >>> report_gen = ReportGeneration() + >>> report_gen.inputs.subject = "sub-01" + >>> report_gen.inputs.session = "ses-01" + >>> report_gen.inputs.stacks = [2,3,5,1] + >>> report_gen.inputs.stacks_order = [5,2,3,1] + >>> report_gen.inputs.sr_id = "1" + >>> report_gen.inputs.run_type = "sr" + >>> report_gen.inputs.output_dir = "report_dir/ + >>> report_gen.inputs.run_start_time = "" + >>> report_gen.inputs.run_elapsed_time = "" + >>> report_gen.inputs.do_refine_hr_mask = True + >>> report_gen.inputs.do_nlm_denoising = True + >>> report_gen.inputs.skip_stacks_ordering = False + >>> report_gen.inputs.skip_svr = False + >>> report_gen.inputs.masks_derivatives_dir = "derivatives/masks" + >>> report_gen.inputs.do_reconstruct_labels = False + >>> report_gen.inputs.do_anat_orientation = True + >>> report_gen.inputs.do_srr_assessment = False + >>> report_gen.inputs.openmp_number_of_cores = 3 + >>> report_gen.inputs.nipype_number_of_cores = 1 + >>> report_gen.inputs.input_sr = "outputs/sub-01_ses-01_res-SR_T2w.nii.gz" + >>> report_gen.inputs.input_json_path = "outputs/sub-01_ses-01_res-SR_T2w.json" + >>> report_gen.run() # doctest: +SKIP + """ input_spec = ReportGenerationInputSpec @@ -1153,7 +1223,7 @@ def _gen_filename(self, name): return None def _run_interface(self, runtime): - """Create the HTML report""" + """Create the HTML report.""" # Set main subject derivatives directory sub_ses = self.inputs.subject sub_path = self.inputs.subject @@ -1267,12 +1337,6 @@ def is_true(x): report_dir = os.path.join(final_res_dir, "report") os.makedirs(report_dir, exist_ok=True) - # Save the HTML report file - # out_report_filename = os.path.join(report_dir, f"{sub_ses}.html") - # - # with open(out_report_filename, "w+") as file: - # file.write(report_html_content) - output_html = self._gen_filename("report_html") print(f"\t* Save HTML report as {output_html}...") with open(output_html, "w+") as f: diff --git a/pymialsrtk/interfaces/preprocess.py b/pymialsrtk/interfaces/preprocess.py index 645e2b90c..17cdcc1de 100644 --- a/pymialsrtk/interfaces/preprocess.py +++ b/pymialsrtk/interfaces/preprocess.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. @@ -21,7 +21,6 @@ # Reorientation -import SimpleITK as sitk import nsol.principal_component_analysis as pca from nipype.algorithms.metrics import Similarity @@ -2028,7 +2027,7 @@ def _list_outputs(self): class ReduceFieldOfViewInputSpec(BaseInterfaceInputSpec): - """Class.""" + """Class used to represent the inputs of the ReduceFieldOfView interface.""" input_image = File(mandatory=True, desc="Input image filename") input_mask = File(mandatory=True, desc="Input mask filename") @@ -2036,7 +2035,7 @@ class ReduceFieldOfViewInputSpec(BaseInterfaceInputSpec): class ReduceFieldOfViewOutputSpec(TraitedSpec): - """Class""" + """Class used to represent the outputs of the ReduceFieldOfView interface.""" output_image = File(desc="Cropped image") output_mask = File(desc="Cropped mask") @@ -2044,7 +2043,17 @@ class ReduceFieldOfViewOutputSpec(TraitedSpec): class ReduceFieldOfView(BaseInterface): - """Runs the""" + """Interface to reduce the Field-of-View. + + Examples + -------- + >>> from pymialsrtk.interfaces.preprocess import ReduceFieldOfView + >>> reduce_fov = ReduceFieldOfView() + >>> reduce_fov.inputs.input_image = 'sub-01_acq-haste_run-1_T2w.nii.gz' + >>> reduce_fov.inputs.input_mask = 'sub-01_acq-haste_run-1_T2w_mask.nii.gz' + >>> reduce_fov.run() # doctest: +SKIP + + """ input_spec = ReduceFieldOfViewInputSpec output_spec = ReduceFieldOfViewOutputSpec @@ -2059,10 +2068,13 @@ def _gen_filename(self, name): return None def _crop_image_and_mask( - self, in_image, in_mask, in_label, paddings_mm=[15, 15, 15] + self, in_image, in_mask, in_label, paddings_mm=None ): import SimpleITK as sitk + if paddings_mm is None: + paddings_mm = [15, 15, 15] + reader = sitk.ImageFileReader() reader.SetFileName(in_mask) @@ -2194,8 +2206,15 @@ class SplitLabelMapsOutputSpec(TraitedSpec): class SplitLabelMaps(BaseInterface): - """Split a multi-label labelmap - into one label map per label. + """Split a multi-label labelmap into one label map per label. + + Examples + -------- + >>> from pymialsrtk.interfaces.preprocess import SplitLabelMaps + >>> split_labels = SplitLabelMaps() + >>> split_labels.inputs.in_labelmap = 'sub-01_acq-haste_run-1_labels.nii.gz' + >>> split_labels.run() # doctest: +SKIP + """ input_spec = SplitLabelMapsInputSpec @@ -2212,6 +2231,8 @@ def _gen_filename(self, name, i): return None def _extractlabelimage(self, in_labelmap): + import SimpleITK as sitk + reader = sitk.ImageFileReader() writer = sitk.ImageFileWriter() @@ -2263,7 +2284,16 @@ class ListsMergerOutputSpec(TraitedSpec): class ListsMerger(BaseInterface): - """Interface to merge list of paths or list of list of path""" + """Interface to merge list of paths or list of list of paths. + + Examples + -------- + >>> from pymialsrtk.interfaces.preprocess import ListsMerger + >>> merge_lists = ListsMerger() + >>> merge_lists.inputs.inputs = ["sub-01_acq-haste_run-1_labels_1.nii.gz", "sub-01_acq-haste_run-1_labels_2.nii.gz"] + >>> merge_lists.run() # doctest: +SKIP + + """ input_spec = ListsMergerInputSpec output_spec = ListsMergerOutputSpec @@ -2313,8 +2343,16 @@ class ResampleImageOutputSpec(TraitedSpec): class ResampleImage(BaseInterface): - """Retrieve atlas of the same age and - resample it to subject's in-plane resolution + """Retrieve atlas of the same age and resample it to subject's in-plane resolution. + + Examples + -------- + >>> from pymialsrtk.interfaces.preprocess import ResampleImage + >>> resample_image = ResampleImage() + >>> resample_image.inputs.input_image = "sub-01_acq-haste_run-1_T2w.nii.gz" + >>> resample_image.inputs.input_reference = "STA30.nii.gz" + >>> resample_image.run() # doctest: +SKIP + """ input_spec = ResampleImageInputSpec @@ -2381,16 +2419,14 @@ def _list_outputs(self): class ComputeAlignmentToReferenceInputSpec(BaseInterfaceInputSpec): - """Class used to represent inputs of the - ComputeAlignmentToReference interface.""" + """Class used to represent inputs of the ComputeAlignmentToReference interface.""" input_image = File(mandatory=True, desc="Input image to realign") input_template = File(mandatory=True, desc="Input reference image") class ComputeAlignmentToReferenceOutputSpec(TraitedSpec): - """Class used to represent outputs of the - ComputeAlignmentToReference interface.""" + """Class used to represent outputs of the ComputeAlignmentToReference interface.""" output_transform = File( mandatory=True, desc="Output 3D rigid tranformation file" @@ -2412,7 +2448,11 @@ class ComputeAlignmentToReference(BaseInterface): Examples -------- - >>> + >>> from pymialsrtk.interfaces.preprocess import ComputeAlignmentToReference + >>> align_to_ref = ComputeAlignmentToReference() + >>> align_to_ref.inputs.input_image = "sub-01_acq-haste_run-1_T2w.nii.gz" + >>> align_to_ref.inputs.input_template = "STA30.nii.gz" + >>> align_to_ref.run() # doctest: +SKIP """ @@ -2444,8 +2484,10 @@ def _list_outputs(self): def _compute_pca(self, mask): def get_largest_connected_region_mask(mask_nda): - """This function is from: - https://github.com/gift-surg/NiftyMIC/blob/e62c5389dfa2bb367fb217b7060472978d3e7654/niftymic/utilities/template_stack_estimator.py#L123 + """This function get the largest connected region mask. + + It originates from https://github.com/gift-surg/NiftyMIC/blob/e62c5389dfa2bb367fb217b7060472978d3e7654/niftymic/utilities/template_stack_estimator.py#L123. + """ # get label for each connected component labels_nda = skimage.measure.label(mask_nda) @@ -2567,8 +2609,7 @@ def _reorient_image(self): class ApplyAlignmentTransformInputSpec(BaseInterfaceInputSpec): - """Class used to represent inputs of the - ApplyAlignmentTransform interface.""" + """Class used to represent inputs of the ApplyAlignmentTransform interface.""" input_image = File(mandatory=True, desc="Input image to realign") input_template = File(mandatory=True, desc="Input reference image") @@ -2581,8 +2622,7 @@ class ApplyAlignmentTransformInputSpec(BaseInterfaceInputSpec): class ApplyAlignmentTransformOutputSpec(TraitedSpec): - """Class used to represent outputs of the - ApplyAlignmentTransform interface.""" + """Class used to represent outputs of the ApplyAlignmentTransform interface.""" output_image = File(mandatory=True, desc="Output reoriented image") output_mask = File(mandatory=False, desc="Output reoriented mask") @@ -2593,7 +2633,13 @@ class ApplyAlignmentTransform(BaseInterface): Examples -------- - >>> + >>> from pymialsrtk.interfaces.preprocess import ApplyAlignmentTransform + >>> align_img = ApplyAlignmentTransform() + >>> align_img.inputs.input_image = "sub-01_acq-haste_run-1_T2w.nii.gz" + >>> align_img.inputs.input_template = "STA30.nii.gz" + >>> align_img.inputs.input_mask = "sub-01_acq-haste_run-1_T2w_mask.nii.gz" + >>> align_img.inputs.input_transform = "sub-01_acq-haste_run-1_rigid.tfm" + >>> align_img.run() # doctest: +SKIP """ @@ -2620,6 +2666,8 @@ def _list_outputs(self): return outputs def _reorient_image(self): + import SimpleITK as sitk + reader = sitk.ImageFileReader() writer = sitk.ImageFileWriter() diff --git a/pymialsrtk/interfaces/reconstruction.py b/pymialsrtk/interfaces/reconstruction.py index 1709445ca..cf0ed4b70 100644 --- a/pymialsrtk/interfaces/reconstruction.py +++ b/pymialsrtk/interfaces/reconstruction.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. @@ -616,8 +616,7 @@ def _list_outputs(self): class MialsrtkSDIComputationInputSpec(BaseInterfaceInputSpec): - """Class used to represent inputs of the - MialsrtkSDIComputation interface.""" + """Class used to represent inputs of the MialsrtkSDIComputation interface.""" input_images = InputMultiPath(File(), desc="Input images", mandatory=True) input_masks = InputMultiPath( @@ -644,17 +643,13 @@ class MialsrtkSDIComputationInputSpec(BaseInterfaceInputSpec): class MialsrtkSDIComputationOutputSpec(TraitedSpec): - """Class used to represent outputs of the - MialsrtkSDIComputation interface.""" + """Class used to represent outputs of the MialsrtkSDIComputation interface.""" output_sdi = File(desc="Output scattered data interpolation image file") class MialsrtkSDIComputation(BaseInterface): - """Creates a high-resolution image - from a set of low resolution images and - their slice-by-slicemotion parameters. - """ + """Creates a high-resolution image from a set of low resolution images and their slice-by-slicemotion parameters.""" input_spec = MialsrtkSDIComputationInputSpec output_spec = MialsrtkSDIComputationOutputSpec @@ -679,9 +674,7 @@ def _gen_filename(self, name): return None def get_empty_ref_image(self, input_ref): - """Generate an empty reference image for - _run_interface - """ + """Generate an empty reference image for `_run_interface`.""" import SimpleITK as sitk reader = sitk.ImageFileReader() @@ -701,7 +694,7 @@ def get_empty_ref_image(self, input_ref): return out_path def _run_interface(self, runtime): - + """Run the MialsrtkSDIComputation interface.""" # Reference image must be empty empty_ref_image = self.get_empty_ref_image(self.inputs.input_reference) params = [] diff --git a/pymialsrtk/interfaces/utils.py b/pymialsrtk/interfaces/utils.py index a1295eaf8..7eb9194c5 100644 --- a/pymialsrtk/interfaces/utils.py +++ b/pymialsrtk/interfaces/utils.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. diff --git a/pymialsrtk/parser.py b/pymialsrtk/parser.py index 38628aa6c..1123c00c8 100644 --- a/pymialsrtk/parser.py +++ b/pymialsrtk/parser.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. @@ -36,7 +36,7 @@ def get_parser(): "--run_type", help="Type of pipeline that is run. Can choose between " "running the super-resolution pipeline (`sr`) " - "or only preprocesing (`preprocessing`).", + "or only preprocessing (`preprocessing`).", choices=["sr", "preprocessing"], default="sr" ) diff --git a/pymialsrtk/pipelines/anatomical/abstract.py b/pymialsrtk/pipelines/anatomical/abstract.py index f3e9dc8da..c65ce0ce5 100644 --- a/pymialsrtk/pipelines/anatomical/abstract.py +++ b/pymialsrtk/pipelines/anatomical/abstract.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. @@ -191,8 +191,7 @@ def create_workflow(self): """ def run(self, memory=None, logger=None): - """Execute the workflow of the super-resolution - reconstruction pipeline. + """Execute the workflow of the super-resolution reconstruction pipeline. Nipype execution engine will take care of the management and execution of all processing steps involved in the super-resolution diff --git a/pymialsrtk/pipelines/anatomical/preprocessing.py b/pymialsrtk/pipelines/anatomical/preprocessing.py index ca29a0df2..b3354ef08 100644 --- a/pymialsrtk/pipelines/anatomical/preprocessing.py +++ b/pymialsrtk/pipelines/anatomical/preprocessing.py @@ -1,4 +1,4 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. @@ -7,7 +7,6 @@ import os -from nipype.info import __version__ as __nipype_version__ from nipype import config from nipype import logging as nipype_logging from nipype.pipeline import engine as pe @@ -15,20 +14,15 @@ import pymialsrtk.interfaces.utils as utils # Import the implemented interface from pymialsrtk -import pymialsrtk.interfaces.reconstruction as reconstruction from pymialsrtk.workflows.input_stage import create_input_stage import pymialsrtk.workflows.preproc_stage as preproc_stage from pymialsrtk.workflows.output_stage import create_preproc_output_stage from pymialsrtk.workflows.registration_stage import create_registration_stage from .abstract import AbstractAnatomicalPipeline -# Get pymialsrtk version -from pymialsrtk.info import __version__ - class PreprocessingPipeline(AbstractAnatomicalPipeline): - """Class used to represent the workflow of the - Preprocessing pipeline. + """Class used to represent the workflow of the Preprocessing pipeline. Attributes ----------- @@ -187,9 +181,10 @@ def __init__( ) def check_parameters_integrity(self, p_dict_custom_interfaces): - """Check whether the custom interfaces dictionary - contains only keys that are used in preprocessing, - and raises an exception if it doesn't. + """Check parameters integrity. + + This checks whether the custom interfaces dictionary contains only keys + that are used in preprocessing, and raises an exception if it doesn't. Parameters ---------- diff --git a/pymialsrtk/pipelines/anatomical/srr.py b/pymialsrtk/pipelines/anatomical/srr.py index b6c9c4399..6d0faa723 100644 --- a/pymialsrtk/pipelines/anatomical/srr.py +++ b/pymialsrtk/pipelines/anatomical/srr.py @@ -1,18 +1,15 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. """Module for the super-resolution reconstruction pipeline.""" import os -import pymialsrtk.interfaces.utils as utils -from nipype.info import __version__ as __nipype_version__ from nipype import config from nipype import logging as nipype_logging from nipype.pipeline import engine as pe # Import the implemented interface from pymialsrtk -import pymialsrtk.interfaces.reconstruction as reconstruction import pymialsrtk.workflows.preproc_stage as preproc_stage import pymialsrtk.workflows.postproc_stage as postproc_stage import pymialsrtk.workflows.srr_assessment_stage as srr_assment_stage @@ -24,8 +21,7 @@ class SRReconPipeline(AbstractAnatomicalPipeline): - """Class used to represent the workflow of the Super-Resolution - reconstruction pipeline. + """Class used to represent the workflow of the Super-Resolution reconstruction pipeline. Attributes ----------- @@ -677,12 +673,14 @@ def create_workflow(self): "inputnode.motion_tsv", ) - def run(self, memory=None): - iflogger = nipype_logging.getLogger("nipype.interface") - res = super().run(memory, iflogger) + def run(self, memory=None, logger=None): + # Use nipype.interface logger to print some information messages + if logger: + iflogger = logger + else: + iflogger = nipype_logging.getLogger("nipype.interface") - # if not self.m_do_multi_parameters: - # iflogger.info("**** Super-resolution HTML report creation ****") - # self.create_subject_report() + # Run the pipeline + res = super().run(memory, iflogger) return res diff --git a/pymialsrtk/workflows/input_stage.py b/pymialsrtk/workflows/input_stage.py index 78d12d1ca..1e5db56c9 100644 --- a/pymialsrtk/workflows/input_stage.py +++ b/pymialsrtk/workflows/input_stage.py @@ -1,11 +1,9 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. -"""Workflow for the management of the input of super-resolution -reconstruction pipeline. -""" +"""Workflow for the management of super-resolution reconstruction pipeline inputs.""" import os import pkg_resources @@ -34,33 +32,61 @@ def create_input_stage( p_verbose, name="input_stage", ): - """Create a input management workflow - for srr pipeline + """Create a input management workflow for srr pipeline. + Parameters ---------- - :: - name : name of workflow (default: input_stage) - p_bids_dir - p_sub_ses - p_use_manual_masks - p_masks_desc - p_masks_derivatives_dir - p_skip_stacks_ordering - p_stacks - p_do_srr_assessment - - Inputs:: - - Outputs:: - outputnode.t2ws_filtered - outputnode.masks_filtered - outputnode.stacks_order - outputnode.report_image - outputnode.motion_tsv - outputnode.ground_truth (optional, if p_do_srr_assessment=True) + name : string + name of workflow (default: input_stage) + p_bids_dir : string + Path to the bids directory + p_sub_ses : string + String containing subject-session information. + p_use_manual_masks : boolean + Whether manual masks are used + p_masks_desc : string + BIDS description tag of masks to use (optional) + p_masks_derivatives_dir : string + Path to the directory of the manual masks. + p_skip_stacks_ordering : boolean + Whether stacks ordering should be skipped. If true, uses the order + provided in `p_stacks`. + p_stacks : list of integer + List of stack to be used in the reconstruction. The specified order is + kept if `skip_stacks_ordering` is True. + p_do_srr_assessment : :obj:`bool` + If super-resolution assessment should be done. + + Outputs + ------- + outputnode.t2ws_filtered : list of filenames + Low-resolution T2w images + outputnode.masks_filtered : list of filenames + Low-resolution T2w masks + outputnode.stacks_order : list of ids + Order in which the stacks should be processed + outputnode.report_image : filename + Output PNG image for report + outputnode.motion_tsv : filename + Output TSV file with results used to create `report_image` + outputnode.ground_truth : filename + Ground truth image used for `srr_assessment` + (optional, if `p_do_srr_assessment=True) + Example ------- - >>> + >>> from pymialsrtk.pipelines.workflows import input_stage + >>> input_mgmt_stage = input_stage.create_input_stage( + p_bids_dir="bids_data", + p_sub_ses="sub-01_ses-1", + p_sub_path="sub-01/ses-1/anat", + p_use_manual_masks=False, + p_skip_stacks_ordering=False, + p_do_srr_assessment=False, + name="input_mgmt_stage", + ) + >>> input_mgmt_stage.run() # doctest: +SKIP + """ input_stage = pe.Workflow(name=name) diff --git a/pymialsrtk/workflows/output_stage.py b/pymialsrtk/workflows/output_stage.py index 54583e72f..fb155069c 100755 --- a/pymialsrtk/workflows/output_stage.py +++ b/pymialsrtk/workflows/output_stage.py @@ -1,11 +1,9 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # This software is distributed under the open-source license Modified BSD. -"""Workflow for the management of the output of super-resolution -reconstruction pipeline.""" +"""Workflow for the management of super-resolution reconstruction pipeline outputs.""" -from pymialsrtk import interfaces from traits.api import * from nipype.interfaces import utility as util from nipype.pipeline import engine as pe @@ -39,8 +37,7 @@ def create_srr_output_stage( p_nipype_number_of_cores=None, name="srr_output_stage", ): - """Create a output management workflow for the - super-resolution reconstruction pipeline. + """Create a output management workflow for the super-resolution reconstruction pipeline. Parameters ---------- @@ -58,7 +55,7 @@ def create_srr_output_stage( Enable non-local means denoising (default: False) p_do_reconstruct_labels: :obj:`bool` Enable the reconstruction of labelmaps - p_do_srr_assessment: :obj:`bool + p_do_srr_assessment: :obj:`bool` Enables output of srr assessment stage p_skip_stacks_ordering : :obj:`bool` Skip stacks ordering (default: False) @@ -70,43 +67,41 @@ def create_srr_output_stage( Inputs ------ - stacks_order + stacks_order : list of integer Order of stacks in the registration (list of integer) - use_manual_masks + use_manual_masks : :obj:`bool` Whether manual masks were used in the pipeline - final_res_dir + final_res_dir : pathlike object or string representing a file Output directory - - input_masks + input_masks : list of items which are a pathlike object or string representing a file Input mask images from the low-resolution T2w images - (list of filenames) - input_images - Input low-resolution T2w images (list of filenames) - input_transforms + input_images : list of items which are a pathlike object or string representing a file + Input low-resolution T2w images + input_transforms : list of items which are a pathlike object or string representing a file Transforms obtained after SVR - input_sdi + input_sdi : pathlike object or string representing a file Interpolated high resolution volume, obtained after slice-to-volume registration (SVR) - input_sr + input_sr : pathlike object or string representing a file High resolution volume, obtained after the super- resolution (SR) reconstruction from the SDI volume. - input_hr_mask + input_hr_mask : pathlike object or string representing a file Brain mask from the high-resolution reconstructed volume. - input_json_path + input_json_path : pathlike object or string representing a file Path to the JSON file describing the parameters used in the SR reconstruction. - input_sr_png + input_sr_png : pathlike object or string representing a file PNG image summarizing the SR reconstruction. - report_image + report_image : pathlike object or string representing a file Report image obtained from the StacksOrdering module - Optional - only if p_skip_stacks_ordering = False - motion_tsv + Optional - only if `p_skip_stacks_ordering = False` + motion_tsv : pathlike object or string representing a file Motion index obtained from the StacksOrdering module - Optional - only if p_skip_stacks_ordering = False - input_images_nlm + Optional - only if `p_skip_stacks_ordering = False` + input_images_nlm : pathlike object or string representing a file Input low-resolution denoised T2w images - Optional - only if p_do_nlm_denoising = True + Optional - only if `p_do_nlm_denoising = True` """ @@ -132,6 +127,12 @@ def create_srr_output_stage( if p_do_multi_parameters: input_fields += ["input_TV_params"] + if not p_run_start_time: + p_run_start_time = 0.0 + + if not p_run_elapsed_time: + p_run_elapsed_time = 0.0 + inputnode = pe.Node( interface=util.IdentityInterface(fields=input_fields), name="inputnode" ) @@ -145,8 +146,8 @@ def create_srr_output_stage( sr_id=p_sr_id, run_type=p_run_type, output_dir=p_output_dir, - run_start_time=0.0, # p_run_start_time, - run_elapsed_time=0.0, # p_run_elapsed_time, + run_start_time=p_run_start_time, + run_elapsed_time=p_run_elapsed_time, skip_svr=p_skip_svr, do_nlm_denoising=p_do_nlm_denoising, do_refine_hr_mask=p_do_refine_hr_mask, @@ -282,57 +283,60 @@ def create_preproc_output_stage( Parameters ---------- - p_sub_ses : + p_sub_ses : string String containing subject-session information for output formatting - p_sr_id : + p_sr_id : integer ID of the current run - p_run_type : - Type of run (preprocessing/super resolution/ ...) - p_use_manual_masks : + p_run_type : "preprocessing" or "super resolution" + Type of run + p_use_manual_masks : boolean Whether manual masks were used in the pipeline - p_do_nlm_denoising : :obj:`bool` - Enable non-local means denoising (default: False) - p_skip_stacks_ordering : :obj:`bool` - Skip stacks ordering (default: False) + p_do_nlm_denoising : boolean + Enable non-local means denoising + (default: False) + p_skip_stacks_ordering : boolean + Skip stacks ordering + (default: False) If disabled, `report_image` and `motion_tsv` are not generated - p_do_registration : :obj:`bool` + p_do_registration : boolean Whether registration is performed in the preprocessing pipeline - name : :obj:`str` - name of workflow (default: "preproc_output_stage") + name : string + name of workflow + (default: "preproc_output_stage") Inputs ------ - sub_ses + sub_ses : string String containing subject-session information for output formatting - sr_id + sr_id : integer ID of the current run - stacks_order + stacks_order : list of integer Order of stacks in the registration (list of integer) - final_res_dir + final_res_dir : pathlike object or string representing a file Output directory - run_type - Type of run (preprocessing/super resolution/ ...) - input_masks + run_type : "preprocessing" or "super resolution" + Type of run + input_masks : list of items which are a pathlike object or string representing a file Input mask images from the low-resolution T2w images - (list of filenames) - input_images - Input low-resolution T2w images (list of filenames) - input_sdi + input_images : list of items which are a pathlike object or string representing a file + Input low-resolution T2w images + input_sdi : pathlike object or string representing a file Interpolated high resolution volume, obtained after slice-to-volume registration (SVR) - Optional - only if p_do_registration = True - input_transforms + Optional - only if `p_do_registration = True` + input_transforms : list of items which are a pathlike object or string representing a file Transforms obtained after SVR - Optional - only if p_do_registration = True - report_image + Optional - only if `p_do_registration = True` + report_image : pathlike object or string representing a file Report image obtained from the StacksOrdering module - Optional - only if p_skip_stacks_ordering = False - motion_tsv + Optional - only if `p_skip_stacks_ordering = False` + motion_tsv : pathlike object or string representing a file Motion index obtained from the StacksOrdering module - Optional - only if p_skip_stacks_ordering = False - input_images_nlm - Input low-resolution denoised T2w images (list of filenames), - Optional - only if p_do_nlm_denoising = True + Optional - only if `p_skip_stacks_ordering = False` + input_images_nlm : list of items which are a pathlike object or string representing a file + Input low-resolution denoised T2w images, + Optional - only if `p_do_nlm_denoising = True` + """ preproc_output_stage = pe.Workflow(name=name) diff --git a/pymialsrtk/workflows/postproc_stage.py b/pymialsrtk/workflows/postproc_stage.py index a08cba9e2..4b40c96ef 100755 --- a/pymialsrtk/workflows/postproc_stage.py +++ b/pymialsrtk/workflows/postproc_stage.py @@ -1,10 +1,9 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. -"""Module for the postprocessing stage of the super-resolution -reconstruction pipeline.""" +"""Module for the postprocessing stage of the super-resolution reconstruction pipeline.""" import numpy as np @@ -18,10 +17,11 @@ def convert_ga(ga): - """Convert the gestational age to - integers between 21 and 38. This is in order to be - able to load the corresponding template using + """Convert the gestational age to integers between 21 and 38. + + This is in order to be able to load the corresponding template using the spatio-temporal atlas of Gholipour et al. + """ ga = int(np.round(ga)) if ga > 38: @@ -39,37 +39,41 @@ def create_postproc_stage( p_verbose=False, name="postproc_stage", ): - """Create a SR preprocessing workflow + """Create a SR preprocessing workflow. + Parameters ---------- - name : :str: - name of workflow (default: preproc_stage) - p_ga: :int: - Subject's gestational age in weeks - p_do_anat_orientation: :bool: - Whether the alignement to template should be performed - p_do_reconstruct_labels: :bool: - Whether the reconstruction of LR labelmaps should be performed - p_verbose: :bool: - Whether verbosity is enabled. + name : string + Name of workflow (default: "preproc_stage") + p_ga : integer + Subject's gestational age in weeks + p_do_anat_orientation : boolean + Whether the alignement to template should be performed + p_do_reconstruct_labels : boolean + Whether the reconstruction of LR labelmaps should be performed + p_verbose : boolean + Whether verbosity is enabled + Inputs ------ - input_sdi: - Input SDI image (filename) - input_image: - Input T2w image (filename) - input_mask: - Input mask image (filename) - input_labelmap: (optional) - Input labelmap image (filename) + input_sdi : pathlike object or string representing a file + Input SDI image + input_image : pathlike object or string representing a file + Input T2w image + input_mask : pathlike object or string representing a file + Input mask image + input_labelmap : pathlike object or string representing a file + Input labelmap image (optional) + Outputs ------- - output_image : - Postprocessed image (filename) - output_mask : - Postprocessed mask (filename) - output_labelmap : - Postprocessed labelmap (filename) + output_image : pathlike object or string representing a file + Postprocessed image + output_mask : pathlike object or string representing a file + Postprocessed mask + output_labelmap : pathlike object or string representing a file + Postprocessed labelmap + """ postproc_stage = pe.Workflow(name=name) diff --git a/pymialsrtk/workflows/preproc_stage.py b/pymialsrtk/workflows/preproc_stage.py index 1c516affd..c43a3b37c 100755 --- a/pymialsrtk/workflows/preproc_stage.py +++ b/pymialsrtk/workflows/preproc_stage.py @@ -1,12 +1,10 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, +# Copyright © 2016-2023 Medical Image Analysis Laboratory, # University Hospital Center and University of # Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. -"""Module for the preprocessing stage of the super-resolution -reconstruction pipeline. -""" +"""Module for the preprocessing stage of the super-resolution reconstruction pipeline.""" from traits.api import * from nipype.interfaces import utility as util @@ -22,37 +20,44 @@ def create_preproc_stage( p_verbose=False, name="preproc_stage", ): - """Create a SR preprocessing workflow + """Create a SR preprocessing workflow. + Parameters ---------- - p_do_nlm_denoising : - Whether to proceed to non-local mean denoising - p_do_reconstruct_labels : - Whether we are also reconstruction label maps. - (default False) - p_verbose : - Whether verbosity should be enabled (default False) - name : - name of workflow (default: preproc_stage) + p_do_nlm_denoising : boolean + Whether to proceed to non-local mean denoising + (default: `False`) + p_do_reconstruct_labels : boolean + Whether we are also reconstruction label maps. + (default: `False`) + p_verbose : boolean + Whether verbosity should be enabled + (default False) + name : string + name of workflow + (default: "preproc_stage") + Inputs ------ - input_images : - Input T2w images (list of filenames) - input_masks : - Input mask images (list of filenames) + input_images : list of items which are a pathlike object or string representing a file + Input T2w images + input_masks : list of items which are a pathlike object or string representing a file + Input mask images + Outputs ------- - output_images : - Processed images (list of filenames) - output_masks : - Processed images (list of filenames) - output_images_nlm : - Processed images with NLM denoising, - if p_do_nlm_denoising was set (list of filenames) + output_images : list of items which are a pathlike object or string representing a file + Processed images + output_masks : list of items which are a pathlike object or string representing a file + Processed images + output_images_nlm : list of items which are a pathlike object or string representing a file + Processed images with NLM denoising, + required if `p_do_nlm_denoising = True` Example ------- - >>> preproc_stage = create_preproc_stage(p_do_nlm_denoising=False) + >>> from pymialsrtk.pipelines.workflows import preproc_stage as preproc + >>> preproc_stage = preproc.create_preproc_stage(p_do_nlm_denoising=False) >>> preproc_stage.inputs.inputnode.input_images = ['sub-01_run-1_T2w.nii.gz', 'sub-01_run-2_T2w.nii.gz'] @@ -60,7 +65,8 @@ def create_preproc_stage( ['sub-01_run-1_T2w_mask.nii.gz', 'sub-01_run-2_T2w_mask.nii.gz'] >>> preproc_stage.inputs.inputnode.p_do_nlm_denoising = 'mask.nii' - >>> preproc_stage.run() # doctest: +SKIP + >>> preproc_stage.run() # doctest: +SKIP + """ preproc_stage = pe.Workflow(name=name) diff --git a/pymialsrtk/workflows/recon_labelmap_stage.py b/pymialsrtk/workflows/recon_labelmap_stage.py index 7841742f9..5ff44690e 100755 --- a/pymialsrtk/workflows/recon_labelmap_stage.py +++ b/pymialsrtk/workflows/recon_labelmap_stage.py @@ -1,53 +1,81 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, +# Copyright © 2016-2023 Medical Image Analysis Laboratory, # University Hospital Center and University of Lausanne (UNIL-CHUV), # Switzerland # # This software is distributed under the open-source license Modified BSD. -"""Module for the high-resolution reconstruction stage -of the low-resolution labelmaps -in the super-resolution reconstruction pipeline.""" +"""Module for the high-resolution reconstruction stage of low-resolution labelmaps in the super-resolution reconstruction pipeline.""" from traits.api import * import pymialsrtk.interfaces.preprocess as preprocess import pymialsrtk.interfaces.postprocess as postprocess import pymialsrtk.interfaces.reconstruction as reconstruction -import pymialsrtk.interfaces.utils as utils from nipype.pipeline import engine as pe from nipype.interfaces import utility as util def create_recon_labelmap_stage( - p_sub_ses, p_verbose, name="recon_labels_stage" + p_sub_ses, p_verbose=False, name="recon_labels_stage" ): - """Create a SR reconstruction workflow - for tissue label maps. + """Create a SR reconstruction workflow for tissue label maps. + Parameters ---------- - p_sub_ses: - p_verbose: - name : name of workflow (default: recon_labels_stage) + p_sub_ses : string + String containing subject-session information for output formatting + p_verbose : boolean + Whether verbosity should be enabled + (default: `False`) + name : string + Name of workflow + (default: "recon_labels_stage") + Inputs ------ - input_labels : - Input LR label maps (list of filenames) - input_masks : - Input mask images (list of filenames) - input_transforms : - Input tranforms (list of filenames) - input_reference : - Input HR reference image (filename) - label_ids : - Label IDs to reconstruct (list of integer) - stacks_order : - Order of stacks in the reconstruction - (list of integer) + input_labels : list of items which are a pathlike object or string representing a file + Input LR label maps + input_masks : list of items which are a pathlike object or string representing a file + Input mask images + input_transforms : list of items which are a pathlike object or string representing a file + Input tranforms + input_reference : pathlike object or string representing a file + Input HR reference image + label_ids : list of integer + Label IDs to reconstruct + stacks_order : list of integer + Order of stacks in the reconstruction + Outputs ------- - output_labelmap : - HR labelmap (filename) + output_labelmap : pathlike object or string representing a file + HR labelmap + + Example + ------- + >>> from pymialsrtk.pipelines.workflows import recon_labelmap_stage as rec_label + >>> recon_labels_stage = rec_label.create_recon_labelmap_stage( + p_sub_ses=p_sub_ses, + p_verbose=p_verbose + ) + >>> recon_labels_stage.inputs.input_labels = [ + 'sub-01_run-1_labels.nii.gz', + 'sub-01_run-2_labels.nii.gz' + ] + >>> recon_labels_stage.inputs.input_masks = [ + 'sub-01_run-1_T2w.nii_mask.gz', + 'sub-01_run-2_T2w.nii_mask.gz' + ] + >>> recon_labels_stage.inputs.input_transforms = [ + 'sub-01_run-1_transforms.txt', + 'sub-01_run-2_transforms.txt' + ] + >>> recon_labels_stage.inputs.input_reference = 'sub-01_desc-GT_T2w.nii.gz' + >>> recon_labels_stage.inputs.label_ids = 'sub-01_desc-GT_T2w.nii.gz' + >>> recon_labels_stage.inputs.stacks_order = [2,1] + >>> recon_labels_stage.run() # doctest: +SKIP + """ recon_labels_stage = pe.Workflow(name=name) diff --git a/pymialsrtk/workflows/recon_stage.py b/pymialsrtk/workflows/recon_stage.py index af6621bd0..bcfde3a01 100644 --- a/pymialsrtk/workflows/recon_stage.py +++ b/pymialsrtk/workflows/recon_stage.py @@ -1,9 +1,8 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # This software is distributed under the open-source license Modified BSD. -"""Module for the reconstruction stage of the super-resolution -reconstruction pipeline.""" +"""Module for the reconstruction stage of the super-resolution reconstruction pipeline.""" from traits.api import * @@ -29,61 +28,74 @@ def create_recon_stage( p_verbose=False, name="recon_stage", ): - """Create a super-resolution reconstruction workflow + """Create a super-resolution reconstruction workflow. + Parameters ---------- - p_paramTV : `obj`:dict: - Dictionary of TV parameters - p_use_manual_masks : - Whether masks were done manually. - p_do_nlm_denoising : - Whether to proceed to non-local mean denoising. - (default False) - p_do_multi_parameters : - p_do_reconstruct_labels : - Whether we are also reconstruction label maps. - (default False) - p_do_refine_hr_mask : - Whether to do high-resolution mask refinement. - (default False) - p_skip_svr : - Whether slice-to-volume registration (SVR) should - be skipped. (default False) - p_sub_ses : - String describing subject-session information - (default '') - p_verbose : - Whether verbosity should be enabled (default False) - name : name of workflow (default: recon_stage) + p_paramTV : dictionary + Dictionary of TV parameters + p_use_manual_masks : boolean + Whether masks were done manually. + p_do_nlm_denoising : boolean + Whether to proceed to non-local mean denoising. + (default: `False`) + p_do_multi_parameters : boolean + Perform super-resolution reconstruction with + a set of multiple parameters. + (default: `False`) + p_do_reconstruct_labels : boolean + Whether we are also reconstruction label maps. + (default: `False`) + p_do_refine_hr_mask : boolean + Whether to do high-resolution mask refinement. + (default: `False`) + p_skip_svr : boolean + Whether slice-to-volume registration (SVR) should + be skipped. + (default: `False`) + p_sub_ses : string + String describing subject-session information + (default: '') + p_verbose : boolean + Whether verbosity should be enabled + (default: `False`) + name : string + Name of workflow + (default: "recon_stage") + Inputs ---------- - input_images : - Input T2w images (list of filenames) - input_images_nlm : - Input T2w images (list of filenames), - if p_do_nlm_denoising was set (list of filenames) - input_masks : - Input mask images (list of filenames) - stacks_order : - Order of stacks in the reconstruction - (list of integer) + input_images : list of items which are a pathlike object or string representing a file + Input T2w images + input_images_nlm : list of items which are a pathlike object or string representing a file + Input T2w images, + required if `p_do_nlm_denoising=True` + input_masks : list of items which are a pathlike object or string representing a file + Input mask images + stacks_order : list of integer + Order of stacks in the reconstruction + Outputs ---------- - output_sr : - SR reconstructed image (filename) - output_sdi : - SDI image (filename) - output_hr_mask : - SRR mask (filename) - output_tranforms : - Transfmation estimated parameters - (list of filenames) - outputnode.output_json_path - outputnode.output_sr_png - outputnode.output_TV_parameters + output_sr : pathlike object or string representing a file + SR reconstructed image + output_sdi : pathlike object or string representing a file + SDI image + output_hr_mask : pathlike object or string representing a file + SRR mask + output_tranforms : list of items which are a pathlike object or string representing a file + Estimated transformation parameters + outputnode.output_json_path : pathlike object or string representing a file + Path to the json sidecar of the SR reconstruction + outputnode.output_sr_png : pathlike object or string representing a file + Path to the PNG of the SR reconstruction + outputnode.output_TV_parameters : dictionary + Parameters used for TV reconstruction + Example ------- - >>> recon_stage = create_preproc_stage( + >>> from pymialsrtk.pipelines.workflows import recon_stage as rec + >>> recon_stage = rec.create_preproc_stage( p_paramTV, p_use_manual_masks, p_do_nlm_denoising=False) @@ -91,8 +103,8 @@ def create_recon_stage( ['sub-01_run-1_T2w.nii.gz', 'sub-01_run-2_T2w.nii.gz'] >>> recon_stage.inputs.inputnode.input_masks = ['sub-01_run-1_T2w_mask.nii.gz', 'sub-01_run-2_T2w_mask.nii.gz'] - >>> recon_stage.inputs.inputnode.p_do_nlm_denoising = 'mask.nii' - >>> recon_stage.run() # doctest: +SKIP + >>> recon_stage.inputs.stacks_order = [2,1] + >>> recon_stage.run() # doctest: +SKIP """ recon_stage = pe.Workflow(name=name) diff --git a/pymialsrtk/workflows/registration_stage.py b/pymialsrtk/workflows/registration_stage.py index f200fea9f..85d07d5e1 100644 --- a/pymialsrtk/workflows/registration_stage.py +++ b/pymialsrtk/workflows/registration_stage.py @@ -1,9 +1,9 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # # This software is distributed under the open-source license Modified BSD. -"""Module for the various parts of workflow pipeline.""" +"""Module for the registration stage of the super-resolution reconstruction pipeline.""" from nipype.pipeline import engine as pe @@ -11,7 +11,6 @@ import pymialsrtk.interfaces.reconstruction as reconstruction # Get pymialsrtk version -from pymialsrtk.info import __version__ from nipype.interfaces import utility as util @@ -22,42 +21,58 @@ def create_registration_stage( p_verbose=False, name="registration_stage", ): - """Create a a registration workflow, used as an optional stage in the - preprocessing only pipeline. + """Create a a registration workflow, used as an optional stage in the preprocessing only pipeline. Parameters ---------- - p_do_nlm_denoising : :obj:`bool` - Enable non-local means denoising (default: False) - p_skip_svr : :obj:`bool` - Skip slice-to-volume registration (default: False) - p_sub_ses : :obj:`str` - String containing subject-session information. - name : :obj:`str` - name of workflow (default: registration_stage) + p_do_nlm_denoising : boolean + Enable non-local means denoising + (default: `False`) + p_skip_svr : boolean + Skip slice-to-volume registration + (default: `False`) + p_sub_ses : string + String containing subject-session information. + name : string + name of workflow + (default: "registration_stage") Inputs ------ - input_images : - Input low-resolution T2w images (list of filenames) - input_images_nlm : - Input low-resolution denoised T2w images (list of filenames), - Optional - only if p_do_nlm_denoising = True - input_masks : - Input mask images from the low-resolution T2w images - (list of filenames) - stacks_order : - Order of stacks in the - registration (list of integer) + input_images : list of items which are a pathlike object or string representing a file + Input low-resolution T2w images + input_images_nlm : list of items which are a pathlike object or string representing a file + Input low-resolution denoised T2w images, + Optional - only if `p_do_nlm_denoising = True` + input_masks : list of items which are a pathlike object or string representing a file + Input mask images from the low-resolution T2w images + stacks_order : list of integer + Order of stacks in the registration Outputs ------- - output_sdi : - SDI image (filename) - output_tranforms : - Transfmation estimated parameters (list of filenames) + output_sdi : pathlike object or string representing a file + SDI image + output_tranforms : list of items which are a pathlike object or string representing a file + Estimated transformation parameters + + Example + ------- + >>> from pymialsrtk.pipelines.workflows import registration_stage as reg + >>> registration_stage = reg.create_registration_stage( + p_sub_ses=p_sub_ses, + ) + >>> registration_stage.inputs.input_images = [ + 'sub-01_run-1_T2w.nii.gz', + 'sub-01_run-2_T2w.nii.gz' + ] + >>> registration_stage.inputs.input_masks = [ + 'sub-01_run-1_T2w.nii_mask.gz', + 'sub-01_run-2_T2w.nii_mask.gz' + ] + >>> registration_stage.inputs.stacks_order = [2,1] + >>> registration_stage.run() # doctest: +SKIP - # doctest: +SKIP """ registration_stage = pe.Workflow(name=name) diff --git a/pymialsrtk/workflows/srr_assessment_stage.py b/pymialsrtk/workflows/srr_assessment_stage.py index 446421065..2c1938bbd 100644 --- a/pymialsrtk/workflows/srr_assessment_stage.py +++ b/pymialsrtk/workflows/srr_assessment_stage.py @@ -1,9 +1,8 @@ -# Copyright © 2016-2021 Medical Image Analysis Laboratory, University Hospital +# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital # Center and University of Lausanne (UNIL-CHUV), Switzerland # This software is distributed under the open-source license Modified BSD. -"""Module for the reconstruction stage of the super-resolution -reconstruction pipeline.""" +"""Module for the assessment of the super-resolution reconstruction quality with a reference.""" from traits.api import * @@ -27,34 +26,66 @@ def create_srr_assessment_stage( p_openmp_number_of_cores=1, name="srr_assessment_stage", ): - """Create an assessment workflow to compare - a SR-reconstructed image and a reference target. + """Create an assessment workflow to compare a SR-reconstructed image and a reference target. Parameters ---------- - :: - name : name of workflow (default: sr_assessment_stage) - p_do_multi_parameters : boolean - whether multiple SR are to be assessed - with different TV parameters(default: False) - p_input_srtv_node : string - when p_do_multi_parameters is set, name of the sourcenode - from which metrics must be merged - p_openmp_number_of_cores : integer - number of threads possible - for ants registration (default : 1) - - Inputs:: - input_reference_image - input_reference_mask - input_reference_labelmap - input_sr_image - input_sdi_image - input_TV_parameters - Outputs:: - outputnode.output_metrics + name : string + Name of workflow + (default: "sr_assessment_stage") + p_do_multi_parameters : boolean + whether multiple SR are to be assessed with different TV parameters + (default: `False`) + p_input_srtv_node : string + when p_do_multi_parameters is set, name of the sourcenode + from which metrics must be merged + p_openmp_number_of_cores : integer + number of threads possible for ants registration + (default : 1) + + Inputs + -------- + input_reference_image : pathlike object or string representing a file + Path to the ground truth image against which the SR will be evaluated. + input_reference_mask : pathlike object or string representing a file + Path to the mask of the ground truth image. + input_reference_labelmap : pathlike object or string representing a file + Path to the labelmap (tissue segmentation) of the ground truth image. + input_sr_image : pathlike object or string representing a file + Path to the SR reconstructed image. + input_sdi_image : pathlike object or string representing a file + Path to the SDI (interpolated image) used as input to the SR. + input_TV_parameters : dictionary + Dictionary of parameters that were used for the TV reconstruction. + + Outputs + -------- + outputnode.output_metrics : list of float + List of output metrics + Example ------- + >>> from pymialsrtk.pipelines.workflows import srr_assessment_stage as srr_assessment + >>> srr_eval = srr_assessment.create_srr_assessment_stage() + >>> srr_eval.inputs.input_reference_image = 'sub-01_desc-GT_T2w.nii.gz' + >>> srr_eval.inputs.input_reference_mask = 'sub-01_desc-GT_mask.nii.gz' + >>> srr_eval.inputs.input_reference_mask = 'sub-01_desc-GT_labels.nii.gz' + >>> srr_eval.inputs.input_sr_image = 'sub-01_id-1_rec-SR_T2w.nii.gz' + >>> srr_eval.inputs.input_sdi_image = 'sub-01_id-1_desc-SDI_T2w.nii.gz' + >>> srr_eval.inputs.input_TV_parameters = { + 'in_loop': '10', + 'in_deltat': '0.01', + 'in_lambda': '0.75', + 'in_bregman_loop': '3', + 'in_iter': '50', + 'in_step_scale': '1', + 'in_gamma': '1', + 'in_inner_thresh': + '1e-05', + 'in_outer_thresh': '1e-06' + } + >>> srr_eval.run() # doctest: +SKIP + """ srr_assessment_stage = pe.Workflow(name=name)