Fix logic to deal with DICOM pixel values below zero (#6)

* clip dicom pixel value to 0 if below 0

* added test cases for the change

* update version

* add build to gitignore

.gitignore

@@ -15,4 +15,7 @@
 /*.egg
 
 # Documentation
-docs/build
+docs/build
+
+# Build
+build/

mritopng/__init__.py

@@ -29,7 +29,8 @@ def mri_to_png(mri_file, png_file):
     for row in image_2d:
         row_scaled = []
         for col in row:
-            col_scaled = int((float(col) / float(max_val)) * 255.0)
+            # cliping pixel value if below 0
+            col_scaled = int((float(max(col, 0)) / float(max_val)) * 255.0)
             row_scaled.append(col_scaled)
         image_2d_scaled.append(row_scaled)
 

setup.py

@@ -9,7 +9,7 @@ def readme():
 
 setup(
     name='mritopng',
-    version='2.0',
+    version='2.1',
     description='Easily convert MRI filed based on the DICOM format to a PNG image',
     long_description=readme(),
     classifiers=[

tests/test_mritopng.py

@@ -8,9 +8,10 @@
 import mritopng
 
 class TestMRIToPNG(unittest.TestCase):
+    """ Basic tests for mritopng """
 
     def test_no_syntax_errors(self):
-        """ A dummy test to make sure the mritopng library got built """
+        """ Test whether mritopng library got built """
         if 'mri_to_png' not in dir(mritopng):
             self.fail()
 
@@ -31,3 +32,27 @@ def test_convert_file(self):
 
         self.assertTrue(filecmp.cmp(actual_path, expected_path),
                         'PNG generated from dicom1 does not match the expected version')
+
+
+    def test_convert_file_with_negative_values(self):
+        """ Tests DICOM files with negative values, which are clipped to 0 """
+
+        cases = ['000012.dcm', '000017.dcm']
+        curr_path = os.path.dirname(os.path.realpath(__file__))
+
+        for case in cases:
+
+            sample_path = os.path.join(curr_path, 'data', 'samples', case)
+            expected_path = os.path.join(curr_path, 'data', 'expected', case + '.png')
+            actual_path = os.path.join(tempfile.gettempdir(), '%s.%s' % (uuid.uuid4(), "png"))
+
+            print('Actual File Path: %s' % actual_path)
+
+            # Try the file conversion
+            try:
+                mritopng.convert_file(sample_path, actual_path)
+            except Exception as err:
+                self.fail('%s' % err)
+
+            self.assertTrue(filecmp.cmp(actual_path, expected_path),
+                            'PNG generated from dicom1 does not match the expected version')