Merge branch 'master' of https://github.com/OpenGATE/GateTools

bin/gt_image_crop

@@ -15,15 +15,15 @@ CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
 @click.option('--output', '-o', help='Output filename', required=True)
 @click.option('--bg', help='Value of the backgroup to autocrop', default=None)
 @click.option('--bb', default=None,
-              help="Bounding Box with 6 ints (voxel), separated with comma 'x1,y1,z1,x2,y2,z2'")
+              help="Bounding Box with 6 ints (voxel), separated with comma 'x1,x2,y1,y2,z1,z2'")
 @gt.add_options(gt.common_options)
 def gt_image_crop(input_filename, output, bg, bb, **kwargs):
     '''
     \b
     Crop an image.
 
     If --bg : auto crop according to the given background value
-    If --bb : manual crop in mm. 
+    If --bb : manual crop in voxel.
 
     \b
     <INPUT_FILENAME> : input image

gatetools/image_convert.py

@@ -190,3 +190,24 @@ def image_convert(inputImage, pixeltype=None):
         return castFilter
 
     return inputImage
+
+#####################################################################################
+import unittest
+import hashlib
+import os
+from .logging_conf import LoggedTestCase
+
+class Test_Convert(LoggedTestCase):
+    def test_convert(self):
+        x = np.arange(-10, 10, 1)
+        y = np.arange(-12, 15, 1)
+        z = np.arange(-13, 10, 1)
+        xx, yy, zz = np.meshgrid(x, y, z)
+        image = itk.image_from_array(np.float32(xx))
+        convertedImage = image_convert(image, "unsigned char")
+        itk.imwrite(convertedImage, "testConvert.mha")
+        with open("testConvert.mha","rb") as fnew:
+            bytesNew = fnew.read()
+            new_hash = hashlib.sha256(bytesNew).hexdigest()
+            os.remove("testConvert.mha")
+            self.assertTrue("da57bf05ec62b9b5ee2aaa71aacbf7dbca8acbf2278553edc499a3af8007dd44" == new_hash)

gatetools/image_crop.py

@@ -117,3 +117,50 @@ def image_crop_with_bb(img, bb):
     cropper.SetRegionOfInterest(region)
     cropper.Update()
     return cropper.GetOutput()
+
+#####################################################################################
+import unittest
+from .logging_conf import LoggedTestCase
+
+class Test_Crop(LoggedTestCase):
+    def test_auto_crop(self):
+        Dimension = 3
+        PixelType = itk.ctype('unsigned char')
+        ImageType = itk.Image[PixelType, Dimension]
+
+        image = ImageType.New()
+        start = itk.Index[Dimension]()
+        start[0] = 0
+        start[1] = 0
+        start[2] = 0
+        size = itk.Size[Dimension]()
+        size[0] = 200
+        size[1] = 200
+        size[2] = 200
+        region = itk.ImageRegion[Dimension]()
+        region.SetSize(size)
+        region.SetIndex(start)
+        image.SetRegions(region)
+        image.Allocate()
+        image.FillBuffer(0)
+        npView = itk.array_from_image(image)
+        npView[10:52, 42:192, 124:147] =1
+        image = itk.image_from_array(npView)
+        autoCrop = image_auto_crop(image)
+        autoCropSize = autoCrop.GetLargestPossibleRegion().GetSize()
+        self.assertTrue(np.allclose(autoCropSize[0], 23))
+        self.assertTrue(np.allclose(autoCropSize[1], 150))
+        self.assertTrue(np.allclose(autoCropSize[2], 42))
+        self.assertTrue(np.allclose(itk.array_from_image(autoCrop)[0, 0, 0], 1))
+    def test_crop(self):
+        x = np.arange(-10, 10, 0.1)
+        y = np.arange(-12, 15, 0.1)
+        z = np.arange(-13, 10, 0.1)
+        xx, yy, zz = np.meshgrid(x, y, z)
+        image = itk.image_from_array(np.float32(xx))
+        croppedImage = image_crop_with_bb(image, gt.bounding_box(xyz=[10.0, 12.0, 0.0, 7.0, 6.0, 15.0]))
+        croppedImageSize = croppedImage.GetLargestPossibleRegion().GetSize()
+        self.assertTrue(np.allclose(croppedImageSize[0], 3))
+        self.assertTrue(np.allclose(croppedImageSize[1], 8))
+        self.assertTrue(np.allclose(croppedImageSize[2], 10))
+        self.assertTrue(np.allclose(itk.array_from_image(croppedImage)[0, 0, 0], -10))

gatetools/phsp/phsp_helpers.py

@@ -377,24 +377,26 @@ def fig_histo2D(ax, data, keys, k, nbins, color='g'):
     ax.set_xlabel(k[0])
     ax.set_ylabel(k[1])
 
-# -----------------------------------------------------------------------------
+#####################################################################################
 import unittest
 import hashlib
-class Test_Phsp(unittest.TestCase):
+from gatetools.logging_conf import LoggedTestCase
+
+class Test_Phsp(LoggedTestCase):
     def test_phsp_convert(self):
-        print('Test_Phsp test_phsp_convert')
         testfilesPath = os.path.dirname(os.path.realpath(__file__))
         testfilesPath = os.path.join(testfilesPath, "testphsp")
         data, read_keys, m = load(os.path.join(testfilesPath, "phsp.root"), -1)
         save_npy(os.path.join(testfilesPath, "testphsp.npy"), data, read_keys)
-        fnew = open(os.path.join(testfilesPath, "testphsp.npy"),"rb")
-        bytesNew = fnew.read()
-        new_hash = hashlib.sha256(bytesNew).hexdigest()
+        with open(os.path.join(testfilesPath, "testphsp.npy"),"rb") as fnew:
+            bytesNew = fnew.read()
+            new_hash = hashlib.sha256(bytesNew).hexdigest()
+            self.assertTrue("cec796ec5764d039b02e15d504e80ccf2b2c35e0e5380985245262faf0ff0892" == new_hash)
+        dataNPY, read_keysNPY, mNPY = load(os.path.join(testfilesPath, "testphsp.npy"), -1)
+        self.assertTrue(np.allclose(131.69868, np.amax(dataNPY[:,2])))
         os.remove(os.path.join(testfilesPath, "testphsp.npy"))
-        self.assertTrue("cec796ec5764d039b02e15d504e80ccf2b2c35e0e5380985245262faf0ff0892" == new_hash)
 
     def test_phsp_info(self):
-        print('Test_Phsp test_phsp_info')
         testfilesPath = os.path.dirname(os.path.realpath(__file__))
         testfilesPath = os.path.join(testfilesPath, "testphsp")
         data, read_keys, m = load(os.path.join(testfilesPath, "phsp.root"), -1)