fixed nii/nrrd pipelines, added plastimatch instructions to README

Author: ccosmin97

README.md

@@ -58,6 +58,7 @@ The AI results shown above can also be found [here](samples/NSCLC_Radiomics_lung
  - pynrrd
  - SimpleITK
  - pyplastimatch
+ - plastimatch
  - scipy
  - scikit-image
  - pandas
@@ -75,6 +76,8 @@ The AI results shown above can also be found [here](samples/NSCLC_Radiomics_lung
 Recommended and supported Python versions are **3.8** and **3.10**.
 Please follow to the installation instructions to ensure reproducibility of this code. The algorithm was developed on Ubuntu 20.04.6 LTS, using Python 3.10.13. GPU used was NVIDIA RTX A6000, 49GB. 
 
+**If you wish to leverage our tool on DICOM data, we internally rely on plastimatch and pyplastimatch tools for DICOM CT to .nrrd/.nii.gz conversion. Please follow the instructions [here](https://github.com/ImagingDataCommons/pyplastimatch?tab=readme-ov-file#plastimatch) for plastimatch installation, depending on your OS.**
+
 ### Windows instructions
 
 ```
@@ -241,7 +244,8 @@ ROCardS --input InputFolder --output OutputFolder
 ```
 
 ### **Single case:**
-- DICOM
+
+ - DICOM
     ```
     ROCardS --input inputDcmFolder --output outputFolder/
 

ROCardS/pyROCardS.py

@@ -48,6 +48,13 @@ def process_dcm_case(inputPath, outFolder, workingDir, df_labels, modelPath):
 
     #DICOM to NRRD to NIFTI
     patSrc  = inputPath
+
+    #make sure input dcm folder has dicom objects
+    try:
+        assert len(glob.glob(os.path.join(inputPath, "*.dcm"))) > 0
+    except:
+        raise Exception(f"no DICOM objects found in case folder : {os.path.join(inputPath)}")
+
     patDst  = os.path.join(workingDir,"dcm_in")
     shutil.copytree(patSrc,patDst)
 
@@ -155,6 +162,7 @@ def main_process_cases(inputPath, outFolder, df_labels, modelPath, verbose=False
         with suppress_output(verbose):
             #init working Dir
             with tempfile.TemporaryDirectory() as workingDir:
+                assert os.path.exists(workingDir)
                 if inputType == "dcm":    
                     #DICOM to NRRD to NIFTI
                     ds = pydicom.dcmread(glob.glob(os.path.join(inputPath, "*.dcm"))[0])
@@ -215,7 +223,7 @@ def main_process_cases(inputPath, outFolder, df_labels, modelPath, verbose=False
                         outFolderCase = os.path.join(outFolder, caseName)
                         os.makedirs(outFolderCase, exist_ok=True)
                         process_nii_case(caseIDPath, outFolderCase, workingDir, 
-                                    df_labels)
+                                    df_labels, modelPath)
 
         elif inputType == "nrrd":
             for caseIDPath in tqdm(sorted(glob.glob(os.path.join(inputPath, "*.nrrd"))), desc="Processing cases"):
@@ -228,7 +236,7 @@ def main_process_cases(inputPath, outFolder, df_labels, modelPath, verbose=False
                         outFolderCase = os.path.join(outFolder, caseName)
                         os.makedirs(outFolderCase, exist_ok=True)
                         process_nrrd_case(caseIDPath, outFolderCase, workingDir, 
-                                    df_labels)
+                                    df_labels, modelPath)
 
         else:
             raise Exception(f"inputType not in nii.gz/nrrd/dcm, please double check your input type.")    

ROCardS/utils_data_process.py

@@ -575,12 +575,12 @@ def detect_input_type_and_format(inputPath : str):
             return (singleCase, inputType)
 
         #multiple cases, either nii(.nii.gz) or nrrd
-        if len(filesLst) > 1 and extLst[0] in ["nii.gz", "nrrd"]:
+        if len(filesLst) >= 1 and extLst[0] in ["nii.gz", "nrrd"]:
             folderCases = True
             singleCase = False
             inputType = extLst[0]
             return (singleCase, inputType)
-    
+            
     #input path is a file
     else:
         folderCases = False

pyproject.toml

@@ -33,13 +33,12 @@ dependencies = [
     "scipy==1.14.1; python_version == '3.10'",
     "scikit-image==0.21.0; python_version in '3.8, 3.9'",
     "scikit-image==0.24.0; python_version == '3.10'",
-    "tensorflow-io-gcs-filesystem==0.34.0; python_version in '3.8, 3.9'",
-    "tensorflow-io-gcs-filesystem==0.37.1; python_version == '3.10'",
+    "tensorflow-io-gcs-filesystem==0.31.0; python_version in '3.8, 3.9, 3.10'",
     "python-gdcm==3.0.24.1; python_version in '3.8, 3.9'"
 ]
 
 [project.urls]
-Homepage = "https://github.com/??/??"
+Homepage = "https://github.com/AIM-Harvard/ROCardS"
 
 [project.scripts]
 ROCardS = "ROCardS.cli.ROCardS:main"

setup.py

@@ -34,7 +34,7 @@
         "pandas==2.3.1; python_version == '3.10'",
         "scipy==1.14.1; python_version == '3.10'",
         "scikit-image==0.24.0; python_version == '3.10'",
-        "tensorflow-io-gcs-filesystem==0.37.1; python_version == '3.10'",
+        "tensorflow-io-gcs-filesystem==0.34.0; python_version == '3.10'",
         # "nvidia-cublas-cu12==12.4.5.8; python_version == '3.10'",
         # "nvidia-cuda-cupti-cu12==12.4.127; python_version == '3.10'",
         # "nvidia-cuda-nvrtc-cu12==12.4.127; python_version == '3.10'",