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Version 2.2.2 update #86

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May 15, 2024
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f966328
Fixed grammar and descriptions.
alexzwanenburg Apr 22, 2024
e3b0a84
Work in progress on new tutorial.
alexzwanenburg Apr 22, 2024
f5e3bb1
New chest CT example dataset.
alexzwanenburg Apr 22, 2024
ade2fd2
Update NEWS.md
alexzwanenburg Apr 22, 2024
d41da9a
Add link to dataset.
alexzwanenburg Apr 22, 2024
104ff8f
Truncate out-of-volume slice_id to the nearest valid value.
alexzwanenburg Apr 23, 2024
c56d360
Add instructions for finding the installed version of MIRP.
alexzwanenburg Apr 23, 2024
c307e94
Add licence and readme to example dataset.
alexzwanenburg Apr 23, 2024
598293f
Nest example image and mask into a folder for better experience
alexzwanenburg Apr 23, 2024
d2a8782
First complete draft of image filter tutorial.
alexzwanenburg Apr 23, 2024
b1addab
Run cells from scratch.
alexzwanenburg Apr 23, 2024
205e941
Remove initial cell.
alexzwanenburg Apr 23, 2024
ea9e141
Added new tutorial to long-form documentation.
alexzwanenburg Apr 23, 2024
1c969a6
Fixed broken links in documentation.
alexzwanenburg Apr 23, 2024
ff673ae
Added link to configuration settings in tutorials #81
alexzwanenburg Apr 23, 2024
c589ae9
Added find_branch method to find xml branches with different names.
alexzwanenburg Apr 23, 2024
699142d
Added missing SUV conversion parameters to documentation.
alexzwanenburg Apr 23, 2024
d30ee7f
Match xml branch names with configuration settings. #81
alexzwanenburg Apr 23, 2024
b3633d2
Better handling of PET units that cannot be converted to BQML. #81
alexzwanenburg Apr 23, 2024
10568c1
Deprecated code that is no longer used.
alexzwanenburg Apr 24, 2024
253bda1
Mask modality is now reported in extract_mask_labels. #81
alexzwanenburg Apr 24, 2024
89bf066
Add missing unit test for extracting mask labels from DICOM SEG objects.
alexzwanenburg Apr 24, 2024
bdb16f8
Deprecate the use of n_labels.
alexzwanenburg Apr 24, 2024
1f89d48
Define default DICOM attributes to export. #81
alexzwanenburg Apr 24, 2024
f21187f
Update tutorials after changes to extract_mask_labels and extract_ima…
alexzwanenburg Apr 24, 2024
12cf61f
Fully document arguments in extract_features, extract_images and simi…
alexzwanenburg Apr 24, 2024
9ab1912
Fixed code generating warnings due to numpy matrix subclass.
alexzwanenburg Apr 24, 2024
2cbc303
Added tests for modality-specific functions #75
alexzwanenburg Apr 24, 2024
1d37c06
Added initial tests for image file descriptors #75
alexzwanenburg Apr 24, 2024
6a96910
Added image descriptor to image and mask import errors and warnings.
alexzwanenburg Apr 25, 2024
01c5363
Added hyperlink to paper references in documentation.
alexzwanenburg Apr 26, 2024
587007d
Update image_descriptors_test.py
alexzwanenburg Apr 26, 2024
070ca92
Add statement of need #73
alexzwanenburg Apr 26, 2024
7246318
WIP on design figure
alexzwanenburg Apr 26, 2024
8ba08fe
Added data citation to tutorial #83
alexzwanenburg May 2, 2024
73b71ad
Work on design documentation.
alexzwanenburg May 3, 2024
aee3263
Update design.rst
alexzwanenburg May 4, 2024
32339af
Extended description of design.
alexzwanenburg May 5, 2024
6e288c2
Details on the internal image representation #73
alexzwanenburg May 5, 2024
0708220
Added descriptions of image and mask representations.
alexzwanenburg May 6, 2024
3caf80a
Added guide to writing tests for contributed code.
alexzwanenburg May 6, 2024
be7a5f5
Updated contributor guide.
alexzwanenburg May 6, 2024
c84b75d
Formatting changes.
alexzwanenburg May 6, 2024
3092322
Added initial feature tables to documentation.
alexzwanenburg May 6, 2024
9f9d377
Added intensity histogram features and intensity volume histogram fea…
alexzwanenburg May 7, 2024
ffea4f0
Added GLCM and GLRLM features #85
alexzwanenburg May 7, 2024
1de0527
Added remaining features and discretisation methods.
alexzwanenburg May 7, 2024
43f0ba4
Update features_names.rst
alexzwanenburg May 7, 2024
2c0b91b
Added some filter descriptors #85
alexzwanenburg May 10, 2024
5ee3ae4
Update features_names.rst
alexzwanenburg May 10, 2024
6cb2bed
Added final transfomations.
alexzwanenburg May 14, 2024
834fce2
Add test to compare between RTSTRUCT and SEG files.
alexzwanenburg May 15, 2024
91f2317
Incremented version to 2.2.2
alexzwanenburg May 15, 2024
45b991d
Update NEWS.md
alexzwanenburg May 15, 2024
7cc5853
Fixed too short lines.
alexzwanenburg May 15, 2024
3f48a67
Fixed header outline.
alexzwanenburg May 15, 2024
e71cd3f
Update documentation.
alexzwanenburg May 15, 2024
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6 changes: 6 additions & 0 deletions .github/ISSUE_TEMPLATE/general-issue.md
Original file line number Diff line number Diff line change
Expand Up @@ -27,3 +27,9 @@ What steps are required to reproduce the problem? If possible, provide code and
- Python version:
- Operating system:
- Other package versions (*if relevant*):

*Hint*: the installed version of MIRP can be found using `importlib_metadata`:
```
import importlib_metadata
importlib_metadata.version("mirp")
```
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -15,3 +15,4 @@ test/data/configuration_files/settings.xml
/docs_source/source/.ipynb_checkpoints
/docs_source/source/sts_images
/prof
/docs_source/source/chest_ct
25 changes: 25 additions & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,28 @@
# Version 2.2.2

## Minor changes

- `show` method of `GenericImage` and subclasses now indicate if a user-provided `slice_id` is out-of-volume and
select the nearest slice instead.

- Naming of branches in the settings `xml` file now matches that of their respective settings classes. `xml` files
with the previous branch names still function.

- Errors encountered during file import and handling are now more descriptive.
- `extract_mask_labels` and `extract_image_parameters` now export extra information from DICOM metadata, e.g. series
UID.

## Documentation

- Added a new tutorial on applying image filters to images.
- Added documentation on the feature naming system.
- Added documentation on the design of MIRP.

## Fixes

- Computing features related to the minimum volume enclosing ellipsoid no longer produces warnings due to the use of
deprecated `numpy.matrix` class.

# Version 2.2.1

## Minor changes
Expand Down
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2 changes: 1 addition & 1 deletion docs/.buildinfo
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@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 9361bdd63c38ffe1be89d15a43241fd1
config: 4e548bc695306a4ce61e35d5a23229c6
tags: 645f666f9bcd5a90fca523b33c5a78b7
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