Packaging4 py pi

dicom2stl.py → dicom2stl/Dicom2STL.py

@@ -21,7 +21,6 @@
 import os
 import sys
 import tempfile
-import shutil
 import time
 import zipfile
 import vtk
@@ -30,12 +29,12 @@
 
 from SimpleITK.utilities.vtk import sitk2vtk
 
-import parseargs
+import dicom2stl
 
 from glob import glob
 
-from utils import dicomutils
-from utils import vtkutils
+from dicom2stl.utils import dicomutils
+from dicom2stl.utils import vtkutils
 
 
 def roundThousand(x):
@@ -89,7 +88,8 @@ def loadVolume(fname, tempDir=None, verbose=0):
             print("zip")
         if not tempDir:
             with tempfile.TemporaryDirectory() as defaultTempDir:
-                img, modality = dicomutils.loadZipDicom(fname[0], defaultTempDir)
+                img, modality = dicomutils.loadZipDicom(fname[0],
+                                                        defaultTempDir)
         else:
             img, modality = dicomutils.loadZipDicom(fname[0], tempDir)
 
@@ -154,7 +154,8 @@ def writeMetadataFile(img, metaName):
 
 
 def volumeProcessingPipeline(
-    img, shrinkFlag=True, anisotropicSmoothing=False, thresholds=[], medianFilter=False
+    img, shrinkFlag=True, anisotropicSmoothing=False, thresholds=[],
+    medianFilter=False
 ):
     #
     # shrink the volume to 256 cubed
@@ -178,8 +179,8 @@ def volumeProcessingPipeline(
 
     gc.collect()
 
-    # Apply anisotropic smoothing to the volume image.  That's a smoothing filter
-    # that preserves edges.
+    # Apply anisotropic smoothing to the volume image.  That's a smoothing
+    # filter that preserves edges.
     #
     if anisotropicSmoothing:
         print("Anisotropic Smoothing")
@@ -197,13 +198,14 @@ def volumeProcessingPipeline(
         print("Double Threshold: ", thresholds)
         t = time.perf_counter()
         img = sitk.DoubleThreshold(
-            img, thresholds[0], thresholds[1], thresholds[2], thresholds[3], 255, 0
+            img, thresholds[0], thresholds[1], thresholds[2], thresholds[3],
+            255, 0
         )
         elapsedTime(t)
         gc.collect()
 
-    # Apply a 3x3x1 median filter.  I only use 1 in the Z direction so it's not so
-    # slow.
+    # Apply a 3x3x1 median filter.  I only use 1 in the Z direction so it's
+    # not so slow.
     #
     if medianFilter:
         print("Median filter")
@@ -297,7 +299,7 @@ def getTissueThresholds(tissueType):
     return thresholds, medianFilter
 
 
-def dicom2stl(args):
+def Dicom2STL(args):
     # Global variables
     #
     thresholds = []
@@ -328,7 +330,7 @@ def dicom2stl(args):
                 rotFlag = val
 
     print("")
-    if args.temp == None:
+    if args.temp is None:
         args.temp = tempfile.mkdtemp()
     print("Temp dir: ", args.temp)
 
@@ -428,8 +430,9 @@ def dicom2stl(args):
 
 
 def main():
-    args = parseargs.parseargs()
-    dicom2stl(args)
+    args = dicom2stl.utils.parseargs.parseargs()
+    Dicom2STL(args)
+
 
 if __name__ == "__main__":
     main()

dicom2stl/__init__.py

@@ -0,0 +1,6 @@
+import dicom2stl
+import dicom2stl.utils.parseargs
+def main():
+    """Entry point for the application script"""
+    args = dicom2stl.utils.parseargs.parseargs()
+    dicom2stl.Dicom2STL(args)

parseargs.py → dicom2stl/utils/parseargs.py

@@ -2,6 +2,16 @@
 
 import argparse
 
+from importlib.metadata import version, PackageNotFoundError
+
+__version__ = "unknown"
+
+try:
+    __version__ = version("dicom2stl")
+except PackageNotFoundError:
+    # package is not installed
+    pass
+
 
 class disableFilter(argparse.Action):
     def __call__(self, parser, args, values, option_string=None):
@@ -104,6 +114,9 @@ def createParser():
         help="Dicom series search string",
     )
 
+    parser.add_argument("--version", action="version", version=f"{__version__}")
+
+
     # Options that apply to the volumetric portion of the pipeline
     vol_group = parser.add_argument_group("Volume options")
 

pyproject.toml

@@ -24,8 +24,11 @@ dynamic = ["dependencies", "version"]
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
 
+[tool.setuptools.packages.find]
+exclude = ["docs*", "tests*", "binder*", "utils*", "examples*", "tmp*"]
+
 [project.scripts]
-dicom2stl = "dicom2stl:main"
+dicom2stl = "dicom2stl.Dicom2STL:main"
 
 [tool.setuptools_scm]
 local_scheme = "dirty-tag"

tests/test_dicom2stl.py

@@ -2,8 +2,8 @@
 import os
 
 import SimpleITK as sitk
-import parseargs
-import dicom2stl
+from dicom2stl.utils import parseargs
+from dicom2stl.Dicom2STL import Dicom2STL
 
 from tests import create_data
 
@@ -34,7 +34,7 @@ def test_dicom2stl(self):
         print(args)
 
         try:
-            dicom2stl.dicom2stl(args)
+            Dicom2STL(args)
         except BaseException:
             self.fail("dicom2stl: exception thrown")
 

tests/test_dicomutils.py

@@ -8,7 +8,7 @@
 import SimpleITK as sitk
 from tests import create_data
 from tests import write_series
-from utils import dicomutils
+from dicom2stl.utils import dicomutils
 
 
 class TestDicomUtils(unittest.TestCase):

tests/test_vtkutils.py

@@ -6,7 +6,7 @@
 import SimpleITK as sitk
 import create_data
 import vtk
-from utils import vtkutils
+from dicom2stl.utils import vtkutils
 
 
 class TestVTKUtils(unittest.TestCase):