DIAGNijmegen/rse-panimg issues and pull requests

#115 - Remove support for Python 3.9

Pull Request - State: closed - Opened by jmsmkn about 1 month ago

#114 - Incompatibility with NumPy 2.x – Binary Incompatibility Error

Issue - State: closed - Opened by larsleijten about 1 month ago - 3 comments

#113 - Correctly mention `.tif` filename suffix as output

Pull Request - State: closed - Opened by chrisvanrun 4 months ago

#112 - Update supported python versions

Pull Request - State: closed - Opened by jmsmkn 4 months ago

#111 - Update python version support and check if this works with PyDicom 3

Issue - State: closed - Opened by jmsmkn 5 months ago

#110 - MHA re-writing takes double the memory of the original image

Issue - State: closed - Opened by jmsmkn 6 months ago - 11 comments

#109 - TypeError: WriteImage() got an unexpected keyword argument 'image'

Issue - State: closed - Opened by j-onne 9 months ago - 1 comment

#108 - changing title of mha file

Issue - State: closed - Opened by j-onne 10 months ago - 5 comments

#107 - Support parsing OME-TIFF format

Issue - State: closed - Opened by chrisvanrun 12 months ago - 2 comments

#106 - Release v0.13.2

Pull Request - State: closed - Opened by miriam-groeneveld over 1 year ago

#105 - Update HISTORY.md

Pull Request - State: closed - Opened by miriam-groeneveld over 1 year ago

#104 - Fix dicom wsi conversion

Pull Request - State: closed - Opened by miriam-groeneveld over 1 year ago

#103 - Fix writing pyramid

Pull Request - State: closed - Opened by miriam-groeneveld over 1 year ago - 6 comments

#102 - changed errors -> file_errors in comment below UnconsumedFilesException

Pull Request - State: closed - Opened by silvandeleemput over 1 year ago
Labels: documentation, enhancement

#101 - Version 0.13.0

Pull Request - State: closed - Opened by jmsmkn over 1 year ago

#100 - Add support for 4D Overlays

Pull Request - State: closed - Opened by jmsmkn over 1 year ago

#99 - Warning when using Pydantic 2

Issue - State: closed - Opened by jmsmkn over 1 year ago - 1 comment

#98 - DICOM Builder picks up WSI DICOM and crashes panimg

Pull Request - State: closed - Opened by GeertLitjens over 1 year ago

#97 - Cannot upload to PyPi

Issue - State: closed - Opened by jmsmkn over 1 year ago - 1 comment

#96 - Fix issues with dependency resolution

Pull Request - State: closed - Opened by jmsmkn over 1 year ago

#95 - Extract min/max sample values from tiff tags

Pull Request - State: closed - Opened by HarmvZ over 1 year ago - 1 comment

#94 - Implement support for DICOM WSI

Pull Request - State: closed - Opened by HarmvZ almost 2 years ago - 1 comment

#93 - Remove usage of `PanImgFolder`

Pull Request - State: closed - Opened by jmsmkn almost 2 years ago

#92 - Release v0.10.0

Pull Request - State: closed - Opened by jmsmkn almost 2 years ago

#91 - Update supported Python versions

Pull Request - State: closed - Opened by jmsmkn almost 2 years ago - 11 comments

#90 - Unknown colour space exception

Issue - State: closed - Opened by jmsmkn over 2 years ago - 8 comments

#89 - Use a frozenset for segments

Pull Request - State: closed - Opened by jmsmkn over 2 years ago

#88 - Add segments property for overlays

Pull Request - State: closed - Opened by MikeOverkamp-diag over 2 years ago

#87 - Correct how the number of timepoints in a 4D scan is determined

Pull Request - State: closed - Opened by nlessmann over 2 years ago

#86 - Release 0.8.3

Pull Request - State: closed - Opened by jmsmkn over 2 years ago

#85 - Move DICOM file sorting into DicomDataset class

Pull Request - State: closed - Opened by nlessmann over 2 years ago - 1 comment

#84 - Catch exceptions that can occur while sorting DICOM files

Pull Request - State: closed - Opened by nlessmann over 2 years ago

#83 - Fix delayed warning about missing OpenSlide installation on Windows

Pull Request - State: closed - Opened by nlessmann over 2 years ago - 1 comment

#82 - Make `post_process` a public method

Pull Request - State: closed - Opened by jmsmkn over 2 years ago

#81 - Unhandled TypeError

Issue - State: closed - Opened by jmsmkn over 2 years ago

#80 - Add mha voxel-value range

Pull Request - State: closed - Opened by chrisvanrun over 2 years ago

#79 - Add support for Python 3.10

Pull Request - State: closed - Opened by jmsmkn almost 3 years ago

#78 - Version 0.8.0

Pull Request - State: closed - Opened by jmsmkn almost 3 years ago

#77 - Group DICOM files differently

Pull Request - State: closed - Opened by nlessmann almost 3 years ago - 8 comments

#76 - Make 'MONOCHROME1' photometric interpretation content dependent

Pull Request - State: closed - Opened by chrisvanrun almost 3 years ago

#75 - Invert also WindowCenter in images with MONOCHROME1 photometric interpretation

Pull Request - State: closed - Opened by nlessmann almost 3 years ago - 1 comment

#74 - ZeroDivisionError in dicom.py

Issue - State: closed - Opened by jmsmkn almost 3 years ago

#73 - Adds photometric interpretation dicom-tag as pass through for DICOMs.

Pull Request - State: closed - Opened by chrisvanrun almost 3 years ago - 3 comments

#72 - Fix reading of X-ray images from DICOM

Pull Request - State: closed - Opened by nlessmann almost 3 years ago

#71 - Restructure DICOM reader to split complex functions up into smaller units

Pull Request - State: closed - Opened by nlessmann almost 3 years ago - 6 comments

#70 - Option to disable header validation

Issue - State: closed - Opened by nlessmann almost 3 years ago - 3 comments

#69 - Release v0.6.0

Pull Request - State: closed - Opened by jmsmkn almost 3 years ago

#68 - Add isort

Pull Request - State: closed - Opened by jmsmkn almost 3 years ago

#67 - Enhanced dicom reading

Pull Request - State: closed - Opened by nlessmann almost 3 years ago - 2 comments

#66 - Validate headers in Nifti and NRRD image builders

Pull Request - State: closed - Opened by nlessmann almost 3 years ago

#65 - CI Standardisation

Pull Request - State: closed - Opened by jmsmkn almost 3 years ago

#64 - Update LICENSE

Pull Request - State: closed - Opened by jmsmkn almost 3 years ago

#63 - Naming of cases imported as dicom files

Issue - State: closed - Opened by EwoudSmit almost 3 years ago - 1 comment

#62 - Update pre-commit dependencies

Pull Request - State: closed - Opened by jmsmkn almost 3 years ago

#61 - Ignore poetry lock file

Pull Request - State: closed - Opened by jmsmkn about 3 years ago - 1 comment

#60 - Calculate slice spacing without assuming axial slices

Pull Request - State: closed - Opened by nlessmann about 3 years ago

#59 - Slice spacing is not calculated correctly if slices are not axial

Issue - State: closed - Opened by nlessmann about 3 years ago

#58 - Require at least numpy 1.21

Pull Request - State: closed - Opened by nlessmann over 3 years ago

#57 - Require at least SimpleITK 2.0

Pull Request - State: closed - Opened by nlessmann over 3 years ago

#56 - Remove duplicate except clause

Pull Request - State: closed - Opened by HarmvZ over 3 years ago

#55 - UnboundLocalError local variable 'simple_itk_image' referenced before assignment

Issue - State: closed - Opened by jmsmkn over 3 years ago
Labels: bug

#54 - Fix extra metadata defaults

Pull Request - State: closed - Opened by HarmvZ over 3 years ago - 1 comment

#53 - Bump version to 0.5.0

Pull Request - State: closed - Opened by HarmvZ over 3 years ago

#52 - Add extra metadata from DICOM and ITK images as fields to PanImg objects

Pull Request - State: closed - Opened by HarmvZ over 3 years ago

#51 - Add extra DICOM and ITK metadata as PanImg fields

Pull Request - State: closed - Opened by HarmvZ over 3 years ago - 1 comment

#50 - Improve existing attribute check for optional metadata fields

Pull Request - State: closed - Opened by HarmvZ over 3 years ago

#49 - Allow for array-like window center and width headers in MHA files

Pull Request - State: closed - Opened by chrisvanrun over 3 years ago - 5 comments

#48 - Simplify 4D ITK loading

Pull Request - State: closed - Opened by chrisvanrun over 3 years ago - 7 comments

#47 - Add image builder for NRRD files

Pull Request - State: closed - Opened by nlessmann over 3 years ago - 2 comments

#46 - Add support for vips 8.10

Pull Request - State: closed - Opened by jmsmkn over 3 years ago

#45 - Allow non-pathology tiff file conversion

Issue - State: open - Opened by HarmvZ over 3 years ago - 5 comments

#44 - Processing 4D MHA results in mangled TransformMatrix

Issue - State: closed - Opened by chrisvanrun over 3 years ago - 9 comments

#43 - Added option to only traverse top-level directory

Pull Request - State: closed - Opened by amickan over 3 years ago

#42 - Add a `recurse_subdirectories: bool = True` kwarg to `convert`

Issue - State: closed - Opened by jmsmkn over 3 years ago

#41 - e2e support

Pull Request - State: closed - Opened by amickan over 3 years ago

#40 - .e2e file support

Issue - State: closed - Opened by amickan over 3 years ago

#39 - Aperio image converted to tiff gets color encoding YCbCr, even when original is RGB

Issue - State: open - Opened by miriam-groeneveld over 3 years ago - 2 comments
Labels: bug

#38 - I got "GDCM is unavailable"

Issue - State: closed - Opened by hihunjin over 3 years ago - 1 comment

#37 - install openslide on ubuntu 18.04

Issue - State: closed - Opened by hihunjin over 3 years ago - 1 comment

#36 - Integrate fds and fda support into panimg

Pull Request - State: closed - Opened by amickan over 3 years ago

#35 - Disable E2E OCT support

Pull Request - State: closed - Opened by HarmvZ over 3 years ago - 1 comment

#34 - Temporarily disable processing of fundus images

Pull Request - State: closed - Opened by HarmvZ over 3 years ago

#33 - Replace gdcm with pylibjpeg

Pull Request - State: closed - Opened by jmsmkn over 3 years ago - 1 comment

#32 - removed fundus image extraction from oct converter

Pull Request - State: closed - Opened by amickan over 3 years ago - 2 comments

#31 - Add click cli

Pull Request - State: closed - Opened by jmsmkn over 3 years ago

#30 - Add a CLI with click

Issue - State: closed - Opened by jmsmkn over 3 years ago

#29 - Move matrix manipulations from oct.py to fds and fda functions

Pull Request - State: closed - Opened by amickan almost 4 years ago - 3 comments

#28 - Removes unused code from oct-converter

Pull Request - State: closed - Opened by jmsmkn almost 4 years ago

#27 - Oct converter added to default image builders

Pull Request - State: closed - Opened by amickan almost 4 years ago - 2 comments

#26 - Avoid division by zero when computing slice spacing when there is only one slice

Pull Request - State: closed - Opened by nlessmann almost 4 years ago - 2 comments

#25 - Release v0.2.1

Pull Request - State: closed - Opened by jmsmkn almost 4 years ago

#24 - Add test for reading enhanced DICOM

Pull Request - State: closed - Opened by nlessmann almost 4 years ago - 2 comments

#23 - Improve support for Enhanced DICOM

Issue - State: closed - Opened by nlessmann almost 4 years ago - 6 comments

#22 - Raise errors only when dependencies are necessary

Pull Request - State: closed - Opened by jmsmkn almost 4 years ago

#21 - Raise import errors only when libopenslide/libvips are actually needed

Pull Request - State: closed - Opened by nlessmann almost 4 years ago - 1 comment

#20 - Make vips and openslide optional dependencies

Issue - State: closed - Opened by nlessmann almost 4 years ago

#19 - Return generators from builders

Pull Request - State: closed - Opened by jmsmkn almost 4 years ago

#18 - Add post processors

Pull Request - State: closed - Opened by jmsmkn almost 4 years ago

#17 - Remove modification of input directories

Pull Request - State: closed - Opened by jmsmkn almost 4 years ago

#16 - Update tifffile

Pull Request - State: closed - Opened by jmsmkn almost 4 years ago

GitHub / DIAGNijmegen/rse-panimg issues and pull requests