mosamatic2 2.0.7__py3-none-any.whl → 2.0.8__py3-none-any.whl

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/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/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/ui/resources/VERSION

@@ -1 +1 @@
-2.0.7 
+2.0.8 

{mosamatic2-2.0.7.dist-info → mosamatic2-2.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.7
+Version: 2.0.8
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl

{mosamatic2-2.0.7.dist-info → mosamatic2-2.0.8.dist-info}/RECORD

@@ -1,9 +1,10 @@
 models.py,sha256=Kx6oWKt7IpTTxrhBDrX61X-ZX12J7yPkJFuhVDsDHoQ,8807
 mosamatic2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/app.py,sha256=RIUa5tvMYFcmEII4xZPLZZdx9dXWqBvwkxkl_R97Jkw,860
-mosamatic2/cli.py,sha256=RTogXBXiYW_EDTmnX7TXx2T22Yth_1AwLFiJP2IUDMc,1289
+mosamatic2/cli.py,sha256=kqLdLCZCA7-xxgOOWohsCCrD6Jz3MamslmCl-41R2rA,1371
 mosamatic2/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/commands/calculatescores.py,sha256=Lb8Q8L2yq7Tt6VBJ6_lltRuldrev_pac6fcgF-xzZyE,1984
+mosamatic2/commands/createdicomsummary.py,sha256=qbVgWGIJPBL8vTBcAxfThloQ_q15OfQy5ohMprzZL4E,1955
 mosamatic2/commands/createpngsfromsegmentations.py,sha256=uUAQJVTqOkBCfENzi21RBNYvf6_nuesx1MeR3j_-7dM,1682
 mosamatic2/commands/dicom2nifti.py,sha256=4hMvglxdOid7p7P_Jc-Tudsf93JRMlYaQsEQctLq2d4,1015
 mosamatic2/commands/rescaledicomimages.py,sha256=25QdCzB5s0sRwkTb3o5zco2bIwy6LttNf7i97kGBDYQ,1280
@@ -45,14 +46,14 @@ mosamatic2/core/tasks/selectslicefromscanstask/__init__.py,sha256=47DEQpj8HBSa-_
 mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py,sha256=1a_QHcIdS4VB39cNEBniaaDzUx3k8DcR0wCtdr8G1d0,4586
 mosamatic2/core/tasks/task.py,sha256=APPnid6dpSGkPuDqU1vm2RIMR5vkpvbP1CPHUMjympg,1691
 mosamatic2/core/utils.py,sha256=zh44FNOWxNKuZ4FcM7VIfMvdlzOr4AA8_PJ1r-6_83k,10855
-mosamatic2/server.py,sha256=jiUc7-aFaDMSY2hg6BhMC9C2FU4V2OrMBSoiIAP8Zcs,4158
+mosamatic2/server.py,sha256=-cZ9BPsZUXoINKqwhCHN8c59mlvzzDXzTVxsYt9au70,4644
 mosamatic2/ui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mosamatic2/ui/mainwindow.py,sha256=nV9RqqSZVoVbU2opJIk7E3n4GvZWtuDETxmzwzmx4mg,13099
 mosamatic2/ui/resources/icons/mosamatic2.icns,sha256=OfhC-diJTIgaNMOezxKKilGsY7mRkaGdU5dGr0MOjIA,2994125
 mosamatic2/ui/resources/icons/mosamatic2.ico,sha256=ySD3RYluHK3pgS0Eas7eKrVk_AskdLQ4qs_IT-wNhq4,12229
 mosamatic2/ui/resources/icons/spinner.gif,sha256=rvaac6GUZauHSPFSOLWr0RmLfjmtZih2Q8knQ2WP3Po,16240
 mosamatic2/ui/resources/images/body-composition.jpg,sha256=KD-BudbXwThB4lJOZZN-ad5-TZRaaZ5cKTH0Ar1TOZs,21227
-mosamatic2/ui/resources/VERSION,sha256=KwH-299m3oBSV3-QDLRQdLqL7fYkxUJhV8qlxIIJb74,8
+mosamatic2/ui/resources/VERSION,sha256=f8DsaK2OdoYvUiYLs5HB9QOzREusf-ClX8iflIy2nY8,8
 mosamatic2/ui/settings.py,sha256=YEVHYJIfNsqMO3v1pjzgh7Pih9GGoUX7S9s8S-sBNUk,2121
 mosamatic2/ui/utils.py,sha256=6bbPIrh4RJ_yhQKNZrgPbL4XeUEogjIjbk_e5c3QS5g,853
 mosamatic2/ui/widgets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -84,7 +85,7 @@ mosamatic2/ui/widgets/panels/visualizations/slicevisualization/slicevisualizatio
 mosamatic2/ui/widgets/panels/visualizations/visualization.py,sha256=JvqTJi7cCGYK1-wrN2oURdCOBoPS2clVUyYglhkoVJg,178
 mosamatic2/ui/widgets/splashscreen.py,sha256=MS-OczOWfwwEQNQd-JWe9_Mh57css0cSQgbu973rwQo,4056
 mosamatic2/ui/worker.py,sha256=v7e3gq7MUudgpB1BJW-P7j5wurzu6-HG5m7I6WHgJp0,699
-mosamatic2-2.0.7.dist-info/entry_points.txt,sha256=MCUpKkgbej1clgp8EqlLQGs0BIKwGPcBPiVWLfGz9Gw,126
-mosamatic2-2.0.7.dist-info/METADATA,sha256=aX9U18Z7h4eR4CR3bRliqeGp8VIwSiBGvw9d42MpowU,1467
-mosamatic2-2.0.7.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-mosamatic2-2.0.7.dist-info/RECORD,,
+mosamatic2-2.0.8.dist-info/entry_points.txt,sha256=MCUpKkgbej1clgp8EqlLQGs0BIKwGPcBPiVWLfGz9Gw,126
+mosamatic2-2.0.8.dist-info/METADATA,sha256=qTtZHQw_rcBOIVlCFKonPY9B2rygwNLf7-IVM8UJJzw,1467
+mosamatic2-2.0.8.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+mosamatic2-2.0.8.dist-info/RECORD,,