mosamatic2 2.0.7__tar.gz → 2.0.9__tar.gz

{mosamatic2-2.0.7 → mosamatic2-2.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.7
+Version: 2.0.9
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl
@@ -10,6 +10,7 @@ Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: antspyx (>=0.5.4)
 Requires-Dist: dicom2nifti (>=2.6.2)
 Requires-Dist: flask (>=3.1.2)
+Requires-Dist: moosez
 Requires-Dist: nibabel (>=5.3.2)
 Requires-Dist: numpy (>=1.26.4)
 Requires-Dist: openpyxl (>=3.1.5)

{mosamatic2-2.0.7 → mosamatic2-2.0.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.7"
+version = "2.0.9"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
@@ -33,6 +33,7 @@ dependencies = [
     "antspyx>=0.5.4",
     "vtk>=9.5.1",
     "pyqtgraph>=0.13.7",
+    "moosez",
 ]
 
 [tool.poetry]

{mosamatic2-2.0.7 → mosamatic2-2.0.9}/src/mosamatic2/cli.py

@@ -6,6 +6,7 @@ from mosamatic2.commands import (
     createpngsfromsegmentations,
     dicom2nifti,
     selectslicefromscans,
+    createdicomsummary,
 )
 from mosamatic2.core.utils import show_doc_command
 
@@ -33,4 +34,5 @@ main.add_command(segmentmusclefatl3tensorflow.segmentmusclefatl3tensorflow)
 main.add_command(createpngsfromsegmentations.createpngsfromsegmentations)
 main.add_command(dicom2nifti.dicom2nifti)
 main.add_command(selectslicefromscans.selectslicefromscans)
+main.add_command(createdicomsummary.createdicomsummary)
 main.add_command(show_doc_command(main)) # Special command to show long description for command

mosamatic2-2.0.9/src/mosamatic2/commands/createdicomsummary.py

@@ -0,0 +1,61 @@
+import click
+
+from mosamatic2.core.tasks import CreateDicomSummaryTask
+
+
+@click.command(help='Creates a DICOM summary inside a root directory')
+@click.option(
+    '--directory', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Root directory with DICOM images (can be multiple scans)',
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def createdicomsummary(directory, output, overwrite):
+    """
+    Creates a DICOM summary inside a root directory. Each patient should have
+    its own directory. Inside each patient's directory, there can be multiple
+    scans (called series) and multiple DICOM files per scan. The output of this
+    command is a file summary.txt (stored in the output directory) that contains
+    the following information:
+
+    - A list of patient directory names with the number of scans inside each
+      patient directory
+    - For each patient directory and scan directory the following information:
+        - Nr. of DICOM images in the scan
+        - Modality (e.g., CT or MRI)
+        - Image type (e.g., for Dixon scans can be in-phase, opposite-phase, 
+          water or fat images)
+        - Rows/columns (size of the images)
+        - Pixel spacing (size of each pixel in mm^2)
+        - Slice thickness: (thickness of each image slice)
+
+    Parameters
+    ----------
+    --directory : str
+        Root directory with patient directories, scans and DICOM images
+
+    --output : str
+        Path to output directory
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = CreateDicomSummaryTask(
+        inputs={'directory': directory},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2-2.0.9/src/mosamatic2/core/data/dicomimage.py

@@ -0,0 +1,27 @@
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.utils import (
+    is_dicom,
+    load_dicom,
+    is_jpeg2000_compressed,
+)
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+
+
+class DicomImage(FileData):
+    def load(self):
+        if self.path():
+            p = load_dicom(self.path())
+            if p:
+                if is_jpeg2000_compressed(p):
+                    p.decompress()
+                self.set_object(p)
+                return True
+            # if is_dicom(self.path()):
+            #     p = load_dicom(self.path())
+            #     if is_jpeg2000_compressed(p):
+            #         p.decompress()
+            #     self.set_object(p)
+            #     return True
+        return False

{mosamatic2-2.0.7 → mosamatic2-2.0.9}/src/mosamatic2/core/pipelines/defaultpipeline/defaultpipeline.py

@@ -8,6 +8,9 @@ from mosamatic2.core.tasks import (
     CreatePngsFromSegmentationsTask,
     CalculateScoresTask,
 )
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
 
 
 class DefaultPipeline(Pipeline):
@@ -25,6 +28,7 @@ class DefaultPipeline(Pipeline):
     ]
     def __init__(self, inputs, params, output, overwrite):
         super(DefaultPipeline, self).__init__(inputs, params, output, overwrite)
+        LOG.info('Found {} images to process'.format(len(os.listdir(self.input('images')))))
         model_type = self.param('model_type')
         # segmentation_task_class = SegmentMuscleFatL3Task if model_type == 'pytorch' else SegmentMuscleFatL3TensorFlowTask
         segmentation_task_class = SegmentMuscleFatL3TensorFlowTask

{mosamatic2-2.0.7 → mosamatic2-2.0.9}/src/mosamatic2/core/tasks/createdicomsummarytask/createdicomsummarytask.py

@@ -25,8 +25,9 @@ class CreateDicomSummaryTask(Task):
             for root, dirs, files in os.walk(patient_dir_path):
                 for f in files:
                     f_path = os.path.join(root, f)
-                    if is_dicom(f_path):
-                        p = load_dicom(f_path, stop_before_pixels=True)
+                    # if is_dicom(f_path):
+                    p = load_dicom(f_path, stop_before_pixels=True)
+                    if p:
                         series_instance_uid = p.SeriesInstanceUID
                         if not series_instance_uid in data[patient_dir_name].keys():
                             data[patient_dir_name][series_instance_uid] = []

{mosamatic2-2.0.7 → mosamatic2-2.0.9}/src/mosamatic2/core/utils.py

@@ -14,10 +14,12 @@ from pydicom.uid import (
     ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian
 )
 from PIL import Image
+from mosamatic2.core.managers.logmanager import LogManager
 
 warnings.filterwarnings("ignore", message="Invalid value for VR UI:", category=UserWarning)
 
 MUSCLE, VAT, SAT = 1, 5, 7
+LOG = LogManager()
 
 
 def create_name_with_timestamp(prefix: str='') -> str:
@@ -102,17 +104,34 @@ def is_dicom(f):
         pydicom.dcmread(f, stop_before_pixels=True)
         return True
     except pydicom.errors.InvalidDicomError:
-        return False
+        try:
+            pydicom.dcmread(f, stop_before_pixels=True, force=True)
+            return True
+        except pydicom.errors.InvalidDicomError:
+            pass
+    return False
     
 
 def load_dicom(f, stop_before_pixels=False):
-    if is_dicom(f):
+    try:
         return pydicom.dcmread(f, stop_before_pixels=stop_before_pixels)
+    except pydicom.errors.InvalidDicomError:
+        try:
+            p = pydicom.dcmread(f, stop_before_pixels=stop_before_pixels, force=True)
+            if hasattr(p, 'SOPClassUID'):
+                if not hasattr(p.file_meta, 'TransferSyntaxUID'):
+                    LOG.warning(f'DICOM file {f} does not have FileMetaData/TransferSyntaxUID, trying to fix...')
+                    p.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
+                return p
+        except pydicom.errors.InvalidDicomError:
+            pass
     return None
 
 
 def is_jpeg2000_compressed(p):
-    return p.file_meta.TransferSyntaxUID not in [ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian]
+    if hasattr(p.file_meta, 'TransferSyntaxUID'):
+        return p.file_meta.TransferSyntaxUID not in [ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian]
+    return False
 
 
 def is_numpy_array(value):

{mosamatic2-2.0.7 → mosamatic2-2.0.9}/src/mosamatic2/server.py

@@ -7,6 +7,7 @@ from mosamatic2.core.tasks import CalculateScoresTask
 from mosamatic2.core.tasks import CreatePngsFromSegmentationsTask
 from mosamatic2.core.tasks import Dicom2NiftiTask
 from mosamatic2.core.tasks import SelectSliceFromScansTask
+from mosamatic2.core.tasks import CreateDicomSummaryTask
 
 app = Flask(__name__)
 
@@ -122,6 +123,21 @@ def run_selectslicefromscans():
     return 'PASSED'
 
 
+@app.route('/createdicomsummary')
+def run_createdicomsummary():
+    directory = request.args.get('directory')
+    output = request.args.get('output')
+    overwrite = request.args.get('overwrite', default=True, type=bool)
+    task = CreateDicomSummaryTask(
+        inputs={'directory': directory},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()
+    return 'PASSED'
+
+
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('--port', type=int, default=constants.MOSAMATIC2_SERVER_PORT)

mosamatic2-2.0.9/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.9 

mosamatic2-2.0.7/src/mosamatic2/core/data/dicomimage.py

@@ -1,18 +0,0 @@
-from mosamatic2.core.data.filedata import FileData
-from mosamatic2.core.utils import (
-    is_dicom,
-    load_dicom,
-    is_jpeg2000_compressed,
-)
-
-
-class DicomImage(FileData):
-    def load(self):
-        if self.path():
-            if is_dicom(self.path()):
-                p = load_dicom(self.path())
-                if is_jpeg2000_compressed(p):
-                    p.decompress()
-                self.set_object(p)
-                return True
-        return False

mosamatic2-2.0.7/src/mosamatic2/ui/resources/VERSION

@@ -1 +0,0 @@
-2.0.7