[BUG] Segmentation Fault

[Gujar-Shubham]

Describe the bug
I am running a few PNG files through the command line and it goes well through some of the samples and then just terminates the entire process without saving the data to the CSV and throws back the Segmentation fault [ core dumped] error.

PyRadiomics configuration
I am using the default param file

PyRadiomics log file
I did get the log file but apparently, the logs were not appended. but here is the terminal output.

(pyrad) sgujar@bino_projects$ pyradiomics sample.csv -o resultsample2.csv -f csv --verbosity 5 --log-file log_text.txt
[2024-05-16 12:59:38] D: radiomics.script: Logging initialized
[2024-05-16 12:59:38] I: radiomics.script: Starting PyRadiomics (version: v3.1.0.post2+g146e3bd)
[2024-05-16 12:59:38] I: radiomics.script: Processing input...
[2024-05-16 12:59:38] D: radiomics.script: Loading batch file "sample.csv"
[2024-05-16 12:59:38] D: radiomics.script: No overrides found
[2024-05-16 12:59:38] I: radiomics.featureextractor: No valid config parameter, using defaults: {'minimumROIDimensions': 2, 'minimumROISize': None, 'normalize': False, 'normalizeScale': 1, 'removeOutliers': None, 'resampledPixelSpacing': None, 'interpolator': 'sitkBSpline', 'preCrop': False, 'padDistance': 5, 'distances': [1], 'force2D': False, 'force2Ddimension': 0, 'resegmentRange': None, 'label': 1, 'additionalInfo': True}
[2024-05-16 12:59:38] I: radiomics.featureextractor: Enabled image types: {'Original': {}}
[2024-05-16 12:59:38] I: radiomics.featureextractor: Enabled features: {'firstorder': [], 'glcm': [], 'gldm': [], 'glrlm': [], 'glszm': [], 'ngtdm': [], 'shape': []}
[2024-05-16 12:59:38] I: radiomics.script: Input valid, starting sequential extraction from 2 case(s)...
[2024-05-16 12:59:38] I: radiomics.script: Processing case 1
[2024-05-16 12:59:38] I: radiomics.featureextractor: Calculating features with label: 255
[2024-05-16 12:59:38] D: radiomics.featureextractor: Enabled images types: {'Original': {}}
[2024-05-16 12:59:38] D: radiomics.featureextractor: Enabled features: {'firstorder': [], 'glcm': [], 'gldm': [], 'glrlm': [], 'glszm': [], 'ngtdm': [], 'shape': []}
[2024-05-16 12:59:38] D: radiomics.featureextractor: Current settings: {'minimumROIDimensions': 2, 'minimumROISize': None, 'normalize': False, 'normalizeScale': 1, 'removeOutliers': None, 'resampledPixelSpacing': None, 'interpolator': 'sitkBSpline', 'preCrop': False, 'padDistance': 5, 'distances': [1], 'force2D': False, 'force2Ddimension': 0, 'resegmentRange': None, 'label': 255, 'additionalInfo': True}
[2024-05-16 12:59:38] I: radiomics.featureextractor: Loading image and mask
[2024-05-16 12:59:39] D: radiomics.imageoperations: Force casting mask to UInt32 to ensure correct datatype.
[2024-05-16 12:59:40] D: radiomics.imageoperations: Checking mask with label 255
[2024-05-16 12:59:40] D: radiomics.imageoperations: Calculating bounding box
[2024-05-16 12:59:40] D: radiomics.imageoperations: Checking minimum number of dimensions requirements (2)
[2024-05-16 12:59:40] D: radiomics.featureextractor: Image and Mask loaded and valid, starting extraction
[2024-05-16 12:59:40] D: radiomics.imageoperations: Cropping to size [2944 4824]
[2024-05-16 12:59:40] W: radiomics.featureextractor: Shape features are only available 3D input (for 2D input, use shape2D). Found 2D input
[2024-05-16 12:59:40] D: radiomics.featureextractor: Creating image type iterator
[2024-05-16 12:59:40] I: radiomics.featureextractor: Adding image type "Original" with custom settings: {}
[2024-05-16 12:59:40] D: radiomics.featureextractor: Extracting features
[2024-05-16 12:59:40] D: radiomics.imageoperations: Yielding original image
[2024-05-16 12:59:40] I: radiomics.featureextractor: Calculating features for original image
[2024-05-16 12:59:40] D: radiomics.imageoperations: Cropping to size [2944 4824]
[2024-05-16 12:59:40] I: radiomics.featureextractor: Computing firstorder
[2024-05-16 12:59:40] D: radiomics.firstorder: Initializing feature class
[2024-05-16 12:59:40] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 12:59:40] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 12:59:41] D: radiomics.firstorder: First order feature class initialized
[2024-05-16 12:59:41] D: radiomics.firstorder: Calculating features
[2024-05-16 12:59:44] I: radiomics.featureextractor: Computing glcm
[2024-05-16 12:59:44] D: radiomics.glcm: Initializing feature class
[2024-05-16 12:59:44] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 12:59:45] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 12:59:45] D: radiomics.glcm: Calculating GLCM matrix in C
[2024-05-16 12:59:46] D: radiomics.glcm: Process calculated matrix
[2024-05-16 12:59:46] D: radiomics.glcm: Create symmetrical matrix
[2024-05-16 12:59:46] D: radiomics.glcm: No empty angles
[2024-05-16 12:59:46] D: radiomics.glcm: Calculating GLCM coefficients
[2024-05-16 13:03:34] D: radiomics.glcm: GLCM feature class initialized, calculated GLCM with shape (1, 2622, 2622, 4)
[2024-05-16 13:03:34] D: radiomics.glcm: Calculating features
[2024-05-16 13:16:11] W: radiomics.glcm: GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
[2024-05-16 13:16:11] I: radiomics.featureextractor: Computing gldm
[2024-05-16 13:16:11] D: radiomics.gldm: Initializing feature class
[2024-05-16 13:16:11] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:16:12] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:16:12] D: radiomics.gldm: Calculating GLDM matrix in C
[2024-05-16 13:16:13] D: radiomics.gldm: Feature class initialized, calculated GLDM with shape (1, 2622, 9)
[2024-05-16 13:16:13] D: radiomics.gldm: Calculating features
[2024-05-16 13:16:13] I: radiomics.featureextractor: Computing glrlm
[2024-05-16 13:16:13] D: radiomics.glrlm: Initializing feature class
[2024-05-16 13:16:13] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:16:13] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:16:14] D: radiomics.glrlm: Calculating GLRLM matrix in C
[2024-05-16 13:16:15] D: radiomics.glrlm: Process calculated matrix
[2024-05-16 13:16:15] D: radiomics.glrlm: No empty angles
[2024-05-16 13:16:15] D: radiomics.glrlm: Calculating GLRLM coefficients
[2024-05-16 13:16:15] D: radiomics.glrlm: GLRLM feature class initialized, calculated GLRLM with shape (1, 2622, 225, 4)
[2024-05-16 13:16:15] D: radiomics.glrlm: Calculating features
[2024-05-16 13:16:16] I: radiomics.featureextractor: Computing glszm
[2024-05-16 13:16:16] D: radiomics.glszm: Initializing feature class
[2024-05-16 13:16:16] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:16:16] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:16:17] D: radiomics.glszm: Calculating GLSZM matrix in C
[2024-05-16 13:16:19] D: radiomics.glszm: Calculating GLSZM coefficients
[2024-05-16 13:16:19] D: radiomics.glszm: GLSZM feature class initialized, calculated GLSZM with shape (1, 2622, 18)
[2024-05-16 13:16:19] D: radiomics.glszm: Calculating features
[2024-05-16 13:16:19] I: radiomics.featureextractor: Computing ngtdm
[2024-05-16 13:16:19] D: radiomics.ngtdm: Initializing feature class
[2024-05-16 13:16:19] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:16:20] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:16:21] D: radiomics.ngtdm: Calculating features
[2024-05-16 13:16:21] D: radiomics.featureextractor: Features extracted
[2024-05-16 13:16:21] I: radiomics.script: Case 1 processed in 0:16:42.779691
[2024-05-16 13:16:21] I: radiomics.script: Processing case 2
[2024-05-16 13:16:21] I: radiomics.featureextractor: Calculating features with label: 255
[2024-05-16 13:16:21] D: radiomics.featureextractor: Enabled images types: {'Original': {}}
[2024-05-16 13:16:21] D: radiomics.featureextractor: Enabled features: {'firstorder': [], 'glcm': [], 'gldm': [], 'glrlm': [], 'glszm': [], 'ngtdm': [], 'shape': []}
[2024-05-16 13:16:21] D: radiomics.featureextractor: Current settings: {'minimumROIDimensions': 2, 'minimumROISize': None, 'normalize': False, 'normalizeScale': 1, 'removeOutliers': None, 'resampledPixelSpacing': None, 'interpolator': 'sitkBSpline', 'preCrop': False, 'padDistance': 5, 'distances': [1], 'force2D': False, 'force2Ddimension': 0, 'resegmentRange': None, 'label': 255, 'additionalInfo': True}
[2024-05-16 13:16:21] I: radiomics.featureextractor: Loading image and mask
[2024-05-16 13:16:21] D: radiomics.imageoperations: Force casting mask to UInt32 to ensure correct datatype.
[2024-05-16 13:16:23] D: radiomics.imageoperations: Checking mask with label 255
[2024-05-16 13:16:23] D: radiomics.imageoperations: Calculating bounding box
[2024-05-16 13:16:23] D: radiomics.imageoperations: Checking minimum number of dimensions requirements (2)
[2024-05-16 13:16:23] D: radiomics.featureextractor: Image and Mask loaded and valid, starting extraction
[2024-05-16 13:16:23] D: radiomics.imageoperations: Cropping to size [3571 6076]
[2024-05-16 13:16:23] W: radiomics.featureextractor: Shape features are only available 3D input (for 2D input, use shape2D). Found 2D input
[2024-05-16 13:16:23] D: radiomics.featureextractor: Creating image type iterator
[2024-05-16 13:16:23] I: radiomics.featureextractor: Adding image type "Original" with custom settings: {}
[2024-05-16 13:16:23] D: radiomics.featureextractor: Extracting features
[2024-05-16 13:16:23] D: radiomics.imageoperations: Yielding original image
[2024-05-16 13:16:23] I: radiomics.featureextractor: Calculating features for original image
[2024-05-16 13:16:23] D: radiomics.imageoperations: Cropping to size [3571 6076]
[2024-05-16 13:16:23] I: radiomics.featureextractor: Computing firstorder
[2024-05-16 13:16:23] D: radiomics.firstorder: Initializing feature class
[2024-05-16 13:16:23] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:16:24] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:16:25] D: radiomics.firstorder: First order feature class initialized
[2024-05-16 13:16:25] D: radiomics.firstorder: Calculating features
[2024-05-16 13:16:30] I: radiomics.featureextractor: Computing glcm
[2024-05-16 13:16:30] D: radiomics.glcm: Initializing feature class
[2024-05-16 13:16:30] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:16:31] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:16:32] D: radiomics.glcm: Calculating GLCM matrix in C
[2024-05-16 13:16:33] D: radiomics.glcm: Process calculated matrix
[2024-05-16 13:16:33] D: radiomics.glcm: Create symmetrical matrix
[2024-05-16 13:16:33] D: radiomics.glcm: No empty angles
[2024-05-16 13:16:33] D: radiomics.glcm: Calculating GLCM coefficients
[2024-05-16 13:21:20] D: radiomics.glcm: GLCM feature class initialized, calculated GLCM with shape (1, 2520, 2520, 4)
[2024-05-16 13:21:20] D: radiomics.glcm: Calculating features
[2024-05-16 13:32:33] W: radiomics.glcm: GLCM is symmetrical, therefore Sum Average = 2 * Joint Average, only 1 needs to be calculated
[2024-05-16 13:32:33] I: radiomics.featureextractor: Computing gldm
[2024-05-16 13:32:33] D: radiomics.gldm: Initializing feature class
[2024-05-16 13:32:33] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:32:34] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:32:35] D: radiomics.gldm: Calculating GLDM matrix in C
[2024-05-16 13:32:36] D: radiomics.gldm: Feature class initialized, calculated GLDM with shape (1, 2520, 9)
[2024-05-16 13:32:36] D: radiomics.gldm: Calculating features
[2024-05-16 13:32:36] I: radiomics.featureextractor: Computing glrlm
[2024-05-16 13:32:36] D: radiomics.glrlm: Initializing feature class
[2024-05-16 13:32:36] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:32:37] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:32:38] D: radiomics.glrlm: Calculating GLRLM matrix in C
[2024-05-16 13:32:40] D: radiomics.glrlm: Process calculated matrix
[2024-05-16 13:32:40] D: radiomics.glrlm: No empty angles
[2024-05-16 13:32:40] D: radiomics.glrlm: Calculating GLRLM coefficients
[2024-05-16 13:32:40] D: radiomics.glrlm: GLRLM feature class initialized, calculated GLRLM with shape (1, 2520, 347, 4)
[2024-05-16 13:32:40] D: radiomics.glrlm: Calculating features
[2024-05-16 13:32:40] I: radiomics.featureextractor: Computing glszm
[2024-05-16 13:32:40] D: radiomics.glszm: Initializing feature class
[2024-05-16 13:32:41] D: radiomics.imageoperations: Discretizing gray levels inside ROI
[2024-05-16 13:32:42] D: radiomics.imageoperations: Calculated 2623 bins for bin width 25 with edges: [ 0 25 50 ... 65525 65550 65575])
[2024-05-16 13:32:42] D: radiomics.glszm: Calculating GLSZM matrix in C
Segmentation fault (core dumped)

To Reproduce
Steps to reproduce the behavior:
I have attached the zip file which has all the images and mask files. there are two samples in this zip. I have also added a sample.csv file into this zip which is the input file.

Expected behavior
I expected that it would run and save all the extracted features to the CSV but it did not and gave me a segmentation fault error.

Version (please complete the following information):

• OS: Linux 5.15.0-102-generic
• Python version: 3.9.19
• PyRadiomics version: v3.1.0.post2+g146e3bd

Additional context
I remember I ran these images a few months back through Pyradiomics and it worked perfectly. I'm not sure where this is a conflicting version issue. maybe someone can run these and confirm if it worked for them using alternative versions would help.

Also when I tried to install pyradiomics using conda it gave me this error
(pyrad) $ conda install -c radiomics pyradiomics
Retrieving notices: ...working... done
Channels:

• radiomics
• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides pykwalify >=1.6.0 needed by pyradiomics-2.0.1b1-py27_0

Could not solve for environment specs
The following packages are incompatible
pyradiomics is not installable because there are no viable options
pyradiomics [2.0.1b1|2.1.0|...|v3.0.1b3] would require
pykwalify >=1.6.0 , which does not exist (perhaps a missing channel);
pyradiomics [3.1.0a1|3.1.0a2|...|v3.1.1a3] would require
libgcc-ng >=12 , which does not exist (perhaps a missing channel).

I don't know if this is related to the segmentation fault. But please let me know.

I am facing this from a long time and have tried multiple troubleshooting attempts.

log_text.txt
segmentationfault_error.zip