Skip to content

Commit 02f5019

Browse files
vicmancrvicmancr
committed
First commit.
0 parents  commit 02f5019

29 files changed

+2348
-0
lines changed

‎.gitignore

+133
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,133 @@
1+
data/*/*
2+
models/*
3+
tests/run*
4+
5+
# Byte-compiled / optimized / DLL files
6+
__pycache__/
7+
*.py[cod]
8+
*$py.class
9+
10+
# C extensions
11+
*.so
12+
13+
# Distribution / packaging
14+
.Python
15+
build/
16+
develop-eggs/
17+
dist/
18+
downloads/
19+
eggs/
20+
.eggs/
21+
lib/
22+
lib64/
23+
parts/
24+
sdist/
25+
var/
26+
wheels/
27+
pip-wheel-metadata/
28+
share/python-wheels/
29+
*.egg-info/
30+
.installed.cfg
31+
*.egg
32+
MANIFEST
33+
34+
# PyInstaller
35+
# Usually these files are written by a python script from a template
36+
# before PyInstaller builds the exe, so as to inject date/other infos into it.
37+
*.manifest
38+
*.spec
39+
40+
# Installer logs
41+
pip-log.txt
42+
pip-delete-this-directory.txt
43+
44+
# Unit test / coverage reports
45+
htmlcov/
46+
.tox/
47+
.nox/
48+
.coverage
49+
.coverage.*
50+
.cache
51+
nosetests.xml
52+
coverage.xml
53+
*.cover
54+
*.py,cover
55+
.hypothesis/
56+
.pytest_cache/
57+
58+
# Translations
59+
*.mo
60+
*.pot
61+
62+
# Django stuff:
63+
*.log
64+
local_settings.py
65+
db.sqlite3
66+
db.sqlite3-journal
67+
68+
# Flask stuff:
69+
instance/
70+
.webassets-cache
71+
72+
# Scrapy stuff:
73+
.scrapy
74+
75+
# Sphinx documentation
76+
docs/_build/
77+
78+
# PyBuilder
79+
target/
80+
81+
# Jupyter Notebook
82+
.ipynb_checkpoints
83+
84+
# IPython
85+
profile_default/
86+
ipython_config.py
87+
88+
# pyenv
89+
.python-version
90+
91+
# pipenv
92+
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
93+
# However, in case of collaboration, if having platform-specific dependencies or dependencies
94+
# having no cross-platform support, pipenv may install dependencies that don't work, or not
95+
# install all needed dependencies.
96+
#Pipfile.lock
97+
98+
# PEP 582; used by e.g. github.com/David-OConnor/pyflow
99+
__pypackages__/
100+
101+
# Celery stuff
102+
celerybeat-schedule
103+
celerybeat.pid
104+
105+
# SageMath parsed files
106+
*.sage.py
107+
108+
# Environments
109+
.env
110+
.venv
111+
env/
112+
venv/
113+
ENV/
114+
env.bak/
115+
venv.bak/
116+
117+
# Spyder project settings
118+
.spyderproject
119+
.spyproject
120+
121+
# Rope project settings
122+
.ropeproject
123+
124+
# mkdocs documentation
125+
/site
126+
127+
# mypy
128+
.mypy_cache/
129+
.dmypy.json
130+
dmypy.json
131+
132+
# Pyre type checker
133+
.pyre/

‎LICENSE

+201
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,201 @@
1+
Apache License
2+
Version 2.0, January 2004
3+
http://www.apache.org/licenses/
4+
5+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
6+
7+
1. Definitions.
8+
9+
"License" shall mean the terms and conditions for use, reproduction,
10+
and distribution as defined by Sections 1 through 9 of this document.
11+
12+
"Licensor" shall mean the copyright owner or entity authorized by
13+
the copyright owner that is granting the License.
14+
15+
"Legal Entity" shall mean the union of the acting entity and all
16+
other entities that control, are controlled by, or are under common
17+
control with that entity. For the purposes of this definition,
18+
"control" means (i) the power, direct or indirect, to cause the
19+
direction or management of such entity, whether by contract or
20+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
21+
outstanding shares, or (iii) beneficial ownership of such entity.
22+
23+
"You" (or "Your") shall mean an individual or Legal Entity
24+
exercising permissions granted by this License.
25+
26+
"Source" form shall mean the preferred form for making modifications,
27+
including but not limited to software source code, documentation
28+
source, and configuration files.
29+
30+
"Object" form shall mean any form resulting from mechanical
31+
transformation or translation of a Source form, including but
32+
not limited to compiled object code, generated documentation,
33+
and conversions to other media types.
34+
35+
"Work" shall mean the work of authorship, whether in Source or
36+
Object form, made available under the License, as indicated by a
37+
copyright notice that is included in or attached to the work
38+
(an example is provided in the Appendix below).
39+
40+
"Derivative Works" shall mean any work, whether in Source or Object
41+
form, that is based on (or derived from) the Work and for which the
42+
editorial revisions, annotations, elaborations, or other modifications
43+
represent, as a whole, an original work of authorship. For the purposes
44+
of this License, Derivative Works shall not include works that remain
45+
separable from, or merely link (or bind by name) to the interfaces of,
46+
the Work and Derivative Works thereof.
47+
48+
"Contribution" shall mean any work of authorship, including
49+
the original version of the Work and any modifications or additions
50+
to that Work or Derivative Works thereof, that is intentionally
51+
submitted to Licensor for inclusion in the Work by the copyright owner
52+
or by an individual or Legal Entity authorized to submit on behalf of
53+
the copyright owner. For the purposes of this definition, "submitted"
54+
means any form of electronic, verbal, or written communication sent
55+
to the Licensor or its representatives, including but not limited to
56+
communication on electronic mailing lists, source code control systems,
57+
and issue tracking systems that are managed by, or on behalf of, the
58+
Licensor for the purpose of discussing and improving the Work, but
59+
excluding communication that is conspicuously marked or otherwise
60+
designated in writing by the copyright owner as "Not a Contribution."
61+
62+
"Contributor" shall mean Licensor and any individual or Legal Entity
63+
on behalf of whom a Contribution has been received by Licensor and
64+
subsequently incorporated within the Work.
65+
66+
2. Grant of Copyright License. Subject to the terms and conditions of
67+
this License, each Contributor hereby grants to You a perpetual,
68+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
69+
copyright license to reproduce, prepare Derivative Works of,
70+
publicly display, publicly perform, sublicense, and distribute the
71+
Work and such Derivative Works in Source or Object form.
72+
73+
3. Grant of Patent License. Subject to the terms and conditions of
74+
this License, each Contributor hereby grants to You a perpetual,
75+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
76+
(except as stated in this section) patent license to make, have made,
77+
use, offer to sell, sell, import, and otherwise transfer the Work,
78+
where such license applies only to those patent claims licensable
79+
by such Contributor that are necessarily infringed by their
80+
Contribution(s) alone or by combination of their Contribution(s)
81+
with the Work to which such Contribution(s) was submitted. If You
82+
institute patent litigation against any entity (including a
83+
cross-claim or counterclaim in a lawsuit) alleging that the Work
84+
or a Contribution incorporated within the Work constitutes direct
85+
or contributory patent infringement, then any patent licenses
86+
granted to You under this License for that Work shall terminate
87+
as of the date such litigation is filed.
88+
89+
4. Redistribution. You may reproduce and distribute copies of the
90+
Work or Derivative Works thereof in any medium, with or without
91+
modifications, and in Source or Object form, provided that You
92+
meet the following conditions:
93+
94+
(a) You must give any other recipients of the Work or
95+
Derivative Works a copy of this License; and
96+
97+
(b) You must cause any modified files to carry prominent notices
98+
stating that You changed the files; and
99+
100+
(c) You must retain, in the Source form of any Derivative Works
101+
that You distribute, all copyright, patent, trademark, and
102+
attribution notices from the Source form of the Work,
103+
excluding those notices that do not pertain to any part of
104+
the Derivative Works; and
105+
106+
(d) If the Work includes a "NOTICE" text file as part of its
107+
distribution, then any Derivative Works that You distribute must
108+
include a readable copy of the attribution notices contained
109+
within such NOTICE file, excluding those notices that do not
110+
pertain to any part of the Derivative Works, in at least one
111+
of the following places: within a NOTICE text file distributed
112+
as part of the Derivative Works; within the Source form or
113+
documentation, if provided along with the Derivative Works; or,
114+
within a display generated by the Derivative Works, if and
115+
wherever such third-party notices normally appear. The contents
116+
of the NOTICE file are for informational purposes only and
117+
do not modify the License. You may add Your own attribution
118+
notices within Derivative Works that You distribute, alongside
119+
or as an addendum to the NOTICE text from the Work, provided
120+
that such additional attribution notices cannot be construed
121+
as modifying the License.
122+
123+
You may add Your own copyright statement to Your modifications and
124+
may provide additional or different license terms and conditions
125+
for use, reproduction, or distribution of Your modifications, or
126+
for any such Derivative Works as a whole, provided Your use,
127+
reproduction, and distribution of the Work otherwise complies with
128+
the conditions stated in this License.
129+
130+
5. Submission of Contributions. Unless You explicitly state otherwise,
131+
any Contribution intentionally submitted for inclusion in the Work
132+
by You to the Licensor shall be under the terms and conditions of
133+
this License, without any additional terms or conditions.
134+
Notwithstanding the above, nothing herein shall supersede or modify
135+
the terms of any separate license agreement you may have executed
136+
with Licensor regarding such Contributions.
137+
138+
6. Trademarks. This License does not grant permission to use the trade
139+
names, trademarks, service marks, or product names of the Licensor,
140+
except as required for reasonable and customary use in describing the
141+
origin of the Work and reproducing the content of the NOTICE file.
142+
143+
7. Disclaimer of Warranty. Unless required by applicable law or
144+
agreed to in writing, Licensor provides the Work (and each
145+
Contributor provides its Contributions) on an "AS IS" BASIS,
146+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
147+
implied, including, without limitation, any warranties or conditions
148+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
149+
PARTICULAR PURPOSE. You are solely responsible for determining the
150+
appropriateness of using or redistributing the Work and assume any
151+
risks associated with Your exercise of permissions under this License.
152+
153+
8. Limitation of Liability. In no event and under no legal theory,
154+
whether in tort (including negligence), contract, or otherwise,
155+
unless required by applicable law (such as deliberate and grossly
156+
negligent acts) or agreed to in writing, shall any Contributor be
157+
liable to You for damages, including any direct, indirect, special,
158+
incidental, or consequential damages of any character arising as a
159+
result of this License or out of the use or inability to use the
160+
Work (including but not limited to damages for loss of goodwill,
161+
work stoppage, computer failure or malfunction, or any and all
162+
other commercial damages or losses), even if such Contributor
163+
has been advised of the possibility of such damages.
164+
165+
9. Accepting Warranty or Additional Liability. While redistributing
166+
the Work or Derivative Works thereof, You may choose to offer,
167+
and charge a fee for, acceptance of support, warranty, indemnity,
168+
or other liability obligations and/or rights consistent with this
169+
License. However, in accepting such obligations, You may act only
170+
on Your own behalf and on Your sole responsibility, not on behalf
171+
of any other Contributor, and only if You agree to indemnify,
172+
defend, and hold each Contributor harmless for any liability
173+
incurred by, or claims asserted against, such Contributor by reason
174+
of your accepting any such warranty or additional liability.
175+
176+
END OF TERMS AND CONDITIONS
177+
178+
APPENDIX: How to apply the Apache License to your work.
179+
180+
To apply the Apache License to your work, attach the following
181+
boilerplate notice, with the fields enclosed by brackets "[]"
182+
replaced with your own identifying information. (Don't include
183+
the brackets!) The text should be enclosed in the appropriate
184+
comment syntax for the file format. We also recommend that a
185+
file or class name and description of purpose be included on the
186+
same "printed page" as the copyright notice for easier
187+
identification within third-party archives.
188+
189+
Copyright 2022 BCN-AIM Universitat de Barcelona
190+
191+
Licensed under the Apache License, Version 2.0 (the "License");
192+
you may not use this file except in compliance with the License.
193+
You may obtain a copy of the License at
194+
195+
http://www.apache.org/licenses/LICENSE-2.0
196+
197+
Unless required by applicable law or agreed to in writing, software
198+
distributed under the License is distributed on an "AS IS" BASIS,
199+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
200+
See the License for the specific language governing permissions and
201+
limitations under the License.

‎Params.yaml

+42
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,42 @@
1+
# This is an example of a parameters file
2+
# It is written according to the YAML-convention (www.yaml.org) and is checked by the code for consistency.
3+
# Three types of parameters are possible and reflected in the structure of the document:
4+
#
5+
# Parameter category:
6+
# Setting Name: <value>
7+
#
8+
# The three parameter categories are:
9+
# - setting: Setting to use for preprocessing and class specific settings. if no <value> is specified, the value for
10+
# this setting is set to None.
11+
# - featureClass: Feature class to enable, <value> is list of strings representing enabled features. If no <value> is
12+
# specified or <value> is an empty list ('[]'), all features for this class are enabled.
13+
# - imageType: image types to calculate features on. <value> is custom kwarg settings (dictionary). if <value> is an
14+
# empty dictionary ('{}'), no custom settings are added for this input image.
15+
#
16+
# Some parameters have a limited list of possible values. Where this is the case, possible values are listed in the
17+
# package documentation
18+
19+
# Settings to use, possible settings are listed in the documentation (section "Customizing the extraction").
20+
setting:
21+
binWidth: 25
22+
label: 1
23+
interpolator: 'sitkBSpline' # This is an enumerated value, here None is not allowed
24+
resampledPixelSpacing: # This disables resampling, as it is interpreted as None, to enable it, specify spacing in x, y, z as [x, y , z]
25+
weightingNorm: # If no value is specified, it is interpreted as None
26+
geometryTolerance: 0.001
27+
28+
# Image types to use: "Original" for unfiltered image, for possible filters, see documentation.
29+
imageType:
30+
Original: {} # for dictionaries / mappings, None values are not allowed, '{}' is interpreted as an empty dictionary
31+
32+
# Featureclasses, from which features must be calculated. If a featureclass is not mentioned, no features are calculated
33+
# for that class. Otherwise, the specified features are calculated, or, if none are specified, all are calculated (excluding redundant/deprecated features).
34+
featureClass:
35+
# redundant Compactness 1, Compactness 2 an Spherical Disproportion features are disabled by default, they can be
36+
# enabled by specifying individual feature names (as is done for glcm) and including them in the list.
37+
shape: []
38+
firstorder: [] # specifying an empty list has the same effect as specifying nothing.
39+
glcm: []
40+
glrlm: []
41+
glszm: []
42+
gldm: [] # contains deprecated features, but as no individual features are specified, the deprecated features are not enabled

‎README.md

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
# Radiomics Features Extractions
2+
Extraction of radiomics features from region of interest (ROI) from medical
3+
images given the segmentation masks.

‎__init__.py

Whitespace-only changes.

‎apps/__init__.py

Whitespace-only changes.

0 commit comments

Comments
 (0)