dbdicom 0.2.0__py3-none-any.whl → 0.2.3__py3-none-any.whl

dbdicom/types/instance.py

@@ -46,10 +46,13 @@ class Instance(Record):
         ds = self.get_dataset()
         return ds.get_pixel_array()
 
-    def set_array(self, 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):
+    def set_pixel_array(self, array): # make private
         ds = self.get_dataset()
         if ds is None:
             ds = new_dataset('MRImage')
@@ -59,7 +62,7 @@ class Instance(Record):
         # 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()
+            self.clear()      
 
     def set_dataset(self, dataset):
         self._key = self.manager.set_instance_dataset(self.uid, dataset, self.key())
@@ -71,20 +74,23 @@ class Instance(Record):
         return map_mask_to(self, target)
 
 
-    def export_as_png(self, path):
-        """Export image in png format."""
-        pixelArray = np.transpose(self.array())
-        centre, width = self.window
-        minValue = centre - width/2
-        maxValue = centre + width/2
-        #cmap = plt.get_cmap(colourTable)
-        cmap = self.colormap
-        if cmap is None:
-            cmap='gray'
-        #plt.imshow(pixelArray, cmap=cmap)
-        plt.imshow(pixelArray, cmap=cmap, vmin=minValue, vmax=maxValue)
-        #plt.imshow(pixelArray, cmap=colourTable)
-        #plt.clim(int(minValue), int(maxValue))
+    def export_as_png(self, path, center=None, width=None, colormap=None):
+        # Export image in png format.
+        if center is None or width is None:
+            c, w = self.window
+        if center is None:
+            center = c
+        if width is None:
+            width = w
+        if colormap is None:
+            colormap = self.colormap
+        if colormap is None:
+            colormap = 'gray'
+
+        vmin = center - width/2
+        vmax = center + width/2
+        array = np.transpose(self.array())
+        plt.imshow(array, cmap=colormap, vmin=vmin, vmax=vmax)
         cBar = plt.colorbar()
         cBar.minorticks_on()
         filename = self.label()
@@ -94,7 +100,7 @@ class Instance(Record):
 
 
     def export_as_csv(self, path):
-        """Export 2D pixel Array in csv format"""
+        # Export 2D pixel Array in csv format
         table = np.transpose(self.array())
         cols = ['Column' + str(x) for x in range(table.shape[0])]
         rows = ['Row' + str(y) for y in range(table.shape[1])]
@@ -105,7 +111,7 @@ class Instance(Record):
 
 
     def export_as_nifti(self, path, affine=None):
-        """Export series as a single Nifty file"""
+        # Export series as a single Nifty file
         ds = self.get_dataset()
         if affine is None:
             affine = ds.get_values('affine_matrix')
@@ -118,6 +124,15 @@ class Instance(Record):
         nib.save(niftiObj, filepath)
 
 
+    def export_as_npy(self, path):
+        # Export instance as a single NPY file
+        array = self.array()
+        filepath = self.label()
+        filepath = os.path.join(path, filepath + '.npy')
+        with open(filepath, 'wb') as f:
+            np.save(f, array)
+
+
     def BGRA_array(self):
         return image.BGRA(
             self.get_pixel_array(),
@@ -125,6 +140,17 @@ class Instance(Record):
             width = self.WindowWidth,
             center = self.WindowCenter,
         )
+    
+    def set_affine(self, affine):
+        p = image.dismantle_affine_matrix(affine)
+        self.read()
+        self.SpacingBetweenSlices = p['SpacingBetweenSlices']
+        self.SliceThickness = p['SpacingBetweenSlices']
+        self.PixelSpacing = p['PixelSpacing']
+        self.ImageOrientationPatient = p['ImageOrientationPatient']
+        self.ImagePositionPatient = p['ImagePositionPatient']
+        self.SliceLocation = np.dot(p['ImagePositionPatient'], p['slice_cosine'])
+        self.clear()
 
 
 def map_to(source, target):
@@ -167,7 +193,7 @@ def map_to(source, target):
 
     return result
 
-
+# Obsolete
 def map_mask_to(record, target):
     """Map non-zero image pixels onto a target image.
     Overwrite pixel values in the target"""