Merge pull request #158 from QIB-Sheffield/development

v0.2.4

dev/sops.txt

@@ -137,14 +137,14 @@ Creating a new release (from a fork)
 Creating a PyPi release
 -----------------------
 
-In the terminal, cd to the /mdreg directory, and:
+In the terminal, cd to the /dbdicom directory, and:
 
 >>> python -m build
 >>> twine upload dist/*
 
 When prompted for user name, enter __token__
 
 As password paste the API token generated in PyPi mdreg repository 
-settings (https://pypi.org/manage/project/mdreg/settings/). 
+settings (https://pypi.org/manage/project/dbdicom/settings/). 
 Note: Paste with Ctrl-V does not work in Windows. Use Edit > Paste via the menu.
 

docs/source/conf.py

@@ -6,9 +6,9 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 project = 'dbdicom'
-copyright = '2022, QIB-Sheffield'
+copyright = '2022-2025, QIB-Sheffield'
 author = 'QIB-Sheffield'
-release = '0.2.3'
+release = '0.2.4'
 
 # -- Path setup --------------------------------------------------------------
 # If extensions (or modules to document with autodoc) are in another directory,

pyproject.toml

@@ -7,7 +7,7 @@ requires = ['setuptools>=61.2']
 
 [project]
 name = "dbdicom"
-version = "0.2.3"
+version = "0.2.4"
 dependencies = [ 
     "matplotlib",
     "nibabel",
@@ -19,6 +19,7 @@ dependencies = [
     "importlib-resources", #necessary?
     'scipy',
     'imageio',
+    'vreg',
 ]
 
 # optional information

requirements.txt

@@ -8,5 +8,4 @@ pydicom
 python-gdcm
 pylibjpeg-libjpeg
 importlib-resources
-scipy
-imageio
+vreg

src/dbdicom/ds/dataset.py

@@ -463,21 +463,22 @@ def new_uid(n=None):
         return [pydicom.uid.generate_uid() for _ in range(n)]
 
 
+# Obsolete - replaced by instance.affine()
 def get_affine_matrix(ds):
     """Affine transformation matrix for a DICOM image"""
 
     # slice_spacing = get_values(ds, 'SpacingBetweenSlices')
     # if slice_spacing is None:
     #     slice_spacing = get_values(ds, 'SliceThickness')
     slice_spacing = get_values(ds, 'SliceThickness')
-
     return image.affine_matrix(
         get_values(ds, 'ImageOrientationPatient'), 
         get_values(ds, 'ImagePositionPatient'), 
         get_values(ds, 'PixelSpacing'), 
         slice_spacing)
 
 
+# Obsolete - replaced by instance.set_affine()
 def set_affine_matrix(ds, affine):
     v = image.dismantle_affine_matrix(affine)
     set_values(ds, 'PixelSpacing', v['PixelSpacing'])

src/dbdicom/extensions/__init__.py

@@ -5,6 +5,5 @@
     scipy, 
     skimage,
     sklearn,
-    vreg,
     matplotlib,
 )

src/dbdicom/extensions/vreg.py

@@ -2,7 +2,7 @@
 import pandas as pd
 import scipy
 import dbdicom
-from dbdicom.utils import vreg
+import vreg
 from dbdicom import Series
 
 

src/dbdicom/types/instance.py

@@ -7,6 +7,7 @@
 import nibabel as nib
 import pandas as pd
 import matplotlib.pyplot as plt
+import vreg
 
 
 from dbdicom.record import Record
@@ -39,31 +40,12 @@ def copy_to_series(self, series):
         uid = self.manager.copy_instance_to_series(self.key(), series.keys(), series)
         return self.record('Instance', uid)
 
-    def array(self):
+    def pixel_values(self):
         return self.get_pixel_array()
 
-    def get_pixel_array(self):
-        ds = self.get_dataset()
-        return ds.get_pixel_array()
-
-    def set_array(self, array): # obsolete
-        self.set_pixel_array(array)
-
     def set_pixel_values(self, array):
         self.set_pixel_array(array)
 
-    def set_pixel_array(self, array): # make private
-        ds = self.get_dataset()
-        if ds is None:
-            ds = new_dataset('MRImage')
-        ds.set_pixel_array(array)
-        in_memory = self.key() in self.manager.dataset
-        self.set_dataset(ds) 
-        # This bit added ad-hoc because set_dataset() places the datset in memory
-        # So if the instance is not in memory, it needs to be written and removed again
-        if not in_memory:
-            self.clear()      
-
     def set_dataset(self, dataset):
         self._key = self.manager.set_instance_dataset(self.uid, dataset, self.key())
 
@@ -141,18 +123,57 @@ def BGRA_array(self):
             center = self.WindowCenter,
         )
 
+    def volume(self):
+        return vreg.volume(self.pixel_values(), 
+                           self.affine())
+
+    def set_volume(self, volume:vreg.Volume3D):
+        self.set_pixel_values(np.squeeze(volume.values))
+        self.set_affine(volume.affine)
+
+    def affine(self):
+        return image.affine_matrix(self.ImageOrientationPatient, 
+                                   self.ImagePositionPatient, 
+                                   self.PixelSpacing, 
+                                   self.SliceThickness)
+
     def set_affine(self, affine):
         p = image.dismantle_affine_matrix(affine)
         self.read()
-        self.SpacingBetweenSlices = p['SpacingBetweenSlices']
-        self.SliceThickness = p['SpacingBetweenSlices']
+        #self.SpacingBetweenSlices = p['SpacingBetweenSlices']
+        self.SliceThickness = p['SliceThickness']
         self.PixelSpacing = p['PixelSpacing']
         self.ImageOrientationPatient = p['ImageOrientationPatient']
         self.ImagePositionPatient = p['ImagePositionPatient']
         self.SliceLocation = np.dot(p['ImagePositionPatient'], p['slice_cosine'])
         self.clear()
 
 
+    # OBSOLETE API
+
+    def array(self):  # obsolete replace by pixel_values
+        return self.get_pixel_array()
+
+    def get_pixel_array(self):  # obsolete replace by pixel_values
+        ds = self.get_dataset()
+        return ds.get_pixel_array()
+
+    def set_array(self, array): # obsolete replace by set_pixel_values
+        self.set_pixel_array(array)
+
+    def set_pixel_array(self, array): # obsolete replace by set_pixel_values
+        ds = self.get_dataset()
+        if ds is None:
+            ds = new_dataset('MRImage')
+        ds.set_pixel_array(array)
+        in_memory = self.key() in self.manager.dataset
+        self.set_dataset(ds) 
+        # This bit added ad-hoc because set_dataset() places the datset in memory
+        # So if the instance is not in memory, it needs to be written and removed again
+        if not in_memory:
+            self.clear()      
+
+
 def map_to(source, target):
     """Map non-zero image pixels onto a target image.