Rename fname to base_name.

qipipe/interfaces/compress.py

@@ -6,7 +6,7 @@
 
 class CompressInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='The file to compress')
-    
+
     dest = Directory(desc='The optional directory to write the compressed file'
                      '(default current directory)')
 
@@ -17,25 +17,25 @@ class CompressOutputSpec(TraitedSpec):
 
 class Compress(BaseInterface):
     input_spec = CompressInputSpec
-    
+
     output_spec = CompressOutputSpec
-    
+
     def _run_interface(self, runtime):
         self.out_file = self._compress(
             self.inputs.in_file, dest=self.inputs.dest)
-        
+
         return runtime
-    
+
     def _list_outputs(self):
         outputs = self._outputs().get()
         outputs['out_file'] = self.out_file
-        
+
         return outputs
-    
+
     def _compress(self, in_file, dest=None):
         """
         Compresses the given file.
-        
+
         :param in_file: the path of the file to compress
         :param dest: the destination (default is the working directory)
         :return: the compressed file path
@@ -44,12 +44,12 @@ def _compress(self, in_file, dest=None):
             dest = os.getcwd()
         if not os.path.exists(dest):
             os.makedirs(dest)
-        _, fname = os.path.split(in_file)
-        out_file = os.path.join(dest, fname + '.gz')
+        _, base_name = os.path.split(in_file)
+        out_file = os.path.join(dest, base_name + '.gz')
         f = open(in_file, 'rb')
         cf = gzip.open(out_file, 'wb')
         cf.writelines(f)
         f.close()
         cf.close()
-        
+
         return os.path.abspath(out_file)

qipipe/interfaces/copy.py

@@ -8,11 +8,11 @@
 class CopyInputSpec(BaseInterfaceInputSpec):
     in_file = traits.Either(File, Directory, exists=True, mandatory=True,
                             desc='The file or directory to copy')
-    
+
     dest = Directory(desc='The destination directory path'
                           ' (default current directory)')
-    
-    out_fname = traits.Either(File, Directory,
+
+    out_base_name = traits.Either(File, Directory,
                               desc='The destination file name'
                                    ' (default is the input file name)')
 
@@ -25,28 +25,28 @@ class CopyOutputSpec(TraitedSpec):
 class Copy(BaseInterface):
     """The Copy interface copies a file to a destination directory."""
     input_spec = CopyInputSpec
-    
+
     output_spec = CopyOutputSpec
-    
+
     def _run_interface(self, runtime):
         self._out_file = self._copy(self.inputs.in_file, self.inputs.dest,
-                                    self.inputs.out_fname)
+                                    self.inputs.out_base_name)
         return runtime
-    
+
     def _list_outputs(self):
         outputs = self._outputs().get()
         outputs['out_file'] = self._out_file
-        
+
         return outputs
-    
-    def _copy(self, in_file, dest=None, out_fname=None):
+
+    def _copy(self, in_file, dest=None, out_base_name=None):
         """
         Copies the given file.
-        
+
         :param in_file: the path of the file or directory to copy
         :param dest: the destination directory path
             (default is the current directory)
-        :param out_fname: the destination file name
+        :param out_base_name: the destination file name
             (default is the input file name)
         :return: the copied file path
         """
@@ -56,16 +56,16 @@ def _copy(self, in_file, dest=None, out_fname=None):
                 os.makedirs(dest)
         else:
             dest = os.getcwd()
-        if out_fname:
+        if out_base_name:
             # Remove the out file name directory.
-            _, out_fname = os.path.split(out_fname)
+            _, out_base_name = os.path.split(out_base_name)
         else:
             # The default out file name is the input file name.
-            _, out_fname = os.path.split(in_file)
-        out_file = os.path.join(dest, out_fname)
+            _, out_base_name = os.path.split(in_file)
+        out_file = os.path.join(dest, out_base_name)
         if os.path.isdir(in_file):
             shutil.copytree(in_file, out_file)
         else:
             shutil.copy(in_file, out_file)
-        
+
         return out_file

qipipe/interfaces/move.py

@@ -45,6 +45,6 @@ def _move(self, in_file, dest):
         if not os.path.exists(dest):
             os.makedirs(dest)
         shutil.move(in_file, dest)
-        _, fname = os.path.split(in_file)
-        out_file = os.path.join(dest, fname)
+        _, base_name = os.path.split(in_file)
+        out_file = os.path.join(dest, base_name)
         return out_file

qipipe/interfaces/preview.py

@@ -8,14 +8,14 @@
 class PreviewInputSpec(BaseInterfaceInputSpec):
     in_file = traits.File(exists=True, mandatory=True,
                           desc='The input 3D NIfTI file')
-    
+
     dest = traits.Directory(desc='The destination directory path'
                                  ' (default current directory)')
-    
+
     crop = traits.List(traits.List(traits.Int),
                        desc='The x and y [min, max] bounds')
-    
-    out_fname = traits.File(desc='The destination file name'
+
+    out_base_name = traits.File(desc='The destination file name'
                                  ' (default is the input file name)')
 
 
@@ -25,32 +25,32 @@ class PreviewOutputSpec(TraitedSpec):
 
 class Preview(BaseInterface):
     """Preview creates a JPEG image from an input DICOM image."""
-    
+
     input_spec = PreviewInputSpec
-    
+
     output_spec = PreviewOutputSpec
-    
+
     def _run_interface(self, runtime):
         self._out_file = self._convert(
             self.inputs.in_file, dest=self.inputs.dest,
-            out_fname=self.inputs.out_fname, crop=self.inputs.crop
+            out_base_name=self.inputs.out_base_name, crop=self.inputs.crop
         )
         return runtime
-    
+
     def _list_outputs(self):
         outputs = self._outputs().get()
         outputs['out_file'] = self._out_file
-        
+
         return outputs
-    
-    def _convert(self, in_file, dest=None, out_fname=None, crop=None):
+
+    def _convert(self, in_file, dest=None, out_base_name=None, crop=None):
         """
         Copies the given file.
-        
+
         :param in_file: the path of the file or directory to copy
         :param dest: the destination directory path
             (default is the current directory)
-        :param out_fname: the destination file name
+        :param out_base_name: the destination file name
             (default is the input file name)
         :param crop: the x and y [min, max] bounds
         :return: the preview JPEG file path
@@ -61,15 +61,15 @@ def _convert(self, in_file, dest=None, out_fname=None, crop=None):
                 os.makedirs(dest)
         else:
             dest = os.getcwd()
-        
+
         # The default output file name is the input file name
         # with a .jpg extension.
-        if not out_fname:
-            _, in_fname = os.path.split(in_file)
-            base, _ = os.path.splitext(in_fname)
-            out_fname = base + '.jpg'
-        out_file = os.path.join(dest, out_fname)
-        
+        if not out_base_name:
+            _, in_base_name = os.path.split(in_file)
+            base, _ = os.path.splitext(in_base_name)
+            out_base_name = base + '.jpg'
+        out_file = os.path.join(dest, out_base_name)
+
         dcm = dicom.read_file(in_file)
         data = dcm.pixel_array
         # Crop the data, if necessary.
@@ -79,5 +79,5 @@ def _convert(self, in_file, dest=None, out_fname=None, crop=None):
             crop_ymin, crop_ymax = crop_y
             data = data[crop_xmin:crop_xmax, crop_ymin:crop_ymax]
         image.imsave(out_file, data, cmap=cm.jet)
-        
+
         return out_file

qipipe/interfaces/uncompress.py

@@ -43,8 +43,8 @@ def _uncompress(self, in_file, dest=None):
             dest = os.getcwd()
         if not os.path.exists(dest):
             os.makedirs(dest)
-        _, fname = os.path.split(in_file)
-        out_file = os.path.join(dest, fname[:-3])
+        _, base_name = os.path.split(in_file)
+        out_file = os.path.join(dest, base_name[:-3])
         cf = gzip.open(in_file, 'rb')
         f = open(out_file, 'wb')
         f.writelines(cf)

qipipe/qiprofile/imaging.py

@@ -201,10 +201,10 @@ def _create_rois(self, xnat_scan, **opts):
         if not rsc.exists():
             return rois
         # The file object label is the file base name.
-        fnames = set(rsc.files().get())
+        base_names = set(rsc.files().get())
         # The mask files do not have _color in the base name.
         # Sort the mask files by the lesion prefix.
-        masks = sorted(f for f in fnames if not '_color' in f)
+        masks = sorted(f for f in base_names if not '_color' in f)
         centroids = opts.get('centroids')
         avg_intensities = opts.get('average_intensities')
         # The color look-up table.
@@ -214,7 +214,7 @@ def _create_rois(self, xnat_scan, **opts):
         for i, mask in enumerate(masks):
             roi_opts = lobel_map_opts.clone()
             label_map_name = label_map_basename(mask)
-            if label_map_name in fnames:
+            if label_map_name in base_names:
                 # A label map must have a color table.
                 if not color_table:
                     raise ImagingUpdateError(
@@ -316,11 +316,11 @@ def _create_modeling(self, resource, scans):
         xnat_file_labels = {xnat_name(xnat_file) for xnat_file in xnat_files}
         result = {}
         for output in OUTPUTS:
-            fname = output + '.nii.gz'
-            if fname in xnat_file_labels:
+            base_name = output + '.nii.gz'
+            if base_name in xnat_file_labels:
                 # TODO - add the param result average and label map to the
                 # pipeline and here.
-                param_result = Modeling.ParameterResult(filename=fname)
+                param_result = Modeling.ParameterResult(filename=base_name)
                 result[output] = param_result
 
         # Return the new qiprofile Modeling object.

qipipe/staging/fix_dicom.py

@@ -122,12 +122,12 @@ def _dest_file_name(in_file, dest):
     :param dest: the destination directory
     :return: the target output file name
     """
-    _, fname = os.path.split(in_file)
+    _, base_name = os.path.split(in_file)
     # Replace non-word characters.
-    fname = re.sub('\W', '_', fname.lower())
+    base_name = re.sub('\W', '_', base_name.lower())
     # Add a .dcm extension, if necessary.
-    _, ext = os.path.splitext(fname)
+    _, ext = os.path.splitext(base_name)
     if not ext:
-        fname = fname + '.dcm'
+        base_name = base_name + '.dcm'
 
-    return os.path.join(dest, fname)
+    return os.path.join(dest, base_name)

qipipe/staging/ohsu.py

@@ -104,7 +104,7 @@
     slice                       # The slice subdirectory
      (?P<slice_sequence_number>\d+)       # The slice index
      /                          # End of the slice subdirectory
-    (?P<fname>                  # The ROI file base name
+    (?P<base_name>                  # The ROI file base name
      .*\.bqf                    # The ROI file extension
     )$                          # End of the ROI file name
 """, re.VERBOSE)
@@ -126,7 +126,7 @@
 SARCOMA_ROI_REGEX = re.compile("""
     ^.*                         # The slice parent directory
     slice(?P<slice_sequence_number>\d+)/  # The slice subdirectory
-    (?P<fname>                  # The ROI file base name
+    (?P<base_name>                  # The ROI file base name
      .*\.bqf                    # The ROI file extension
     )$                          # End of the ROI file name
 """, re.VERBOSE)

test/unit/interfaces/test_copy.py

@@ -43,7 +43,7 @@ def test_copy_file(self):
 
     def test_copy_file_with_output_filename(self):
         # Copy the file.
-        copy = Copy(in_file=SOURCE, dest=TARGET, out_fname='target.txt')
+        copy = Copy(in_file=SOURCE, dest=TARGET, out_base_name='target.txt')
         result = copy.run()
 
         # Verify the result.

test/unit/interfaces/test_xnat_copy.py

@@ -59,14 +59,14 @@ def test_scan(self):
             scan_obj = xnat.find_one(PROJECT, SUBJECT, SESSION, scan=SCAN)
             assert_is_not_none(scan_obj, "Upload did not create the %s %s scan:"
                                       " %s" % (SUBJECT, SESSION, SCAN))
-            _, fname = os.path.split(FIXTURE)
-            assert_in(fname, xnat_files,
+            _, base_name = os.path.split(FIXTURE)
+            assert_in(base_name, xnat_files,
                       "The XNATCopy result does not include the %s %s scan"
-                      " %d file %s" % (SUBJECT, SESSION, SCAN, fname))
-            file_obj = scan_obj.resource('NIFTI').file(fname)
+                      " %d file %s" % (SUBJECT, SESSION, SCAN, base_name))
+            file_obj = scan_obj.resource('NIFTI').file(base_name)
             assert_true(file_obj.exists(),
                         "XNATCopy did not create the %s %s scan %d file: %s" %
-                        (SUBJECT, SESSION, SCAN, fname))
+                        (SUBJECT, SESSION, SCAN, base_name))
 
     def test_registration(self):
         logger(__name__).debug("Testing the XNATCopy interface on %s %s"
@@ -87,11 +87,11 @@ def test_registration(self):
             assert_true(rsc_obj.exists(),
                         "XNATCopy did not create the %s %s resource: %s" %
                         (SUBJECT, SESSION, REGISTRATION))
-            _, fname = os.path.split(FIXTURE)
-            file_obj = rsc_obj.file(fname)
+            _, base_name = os.path.split(FIXTURE)
+            file_obj = rsc_obj.file(base_name)
             assert_true(file_obj.exists(),
                         "XNATCopy did not create the %s %s %s file: %s" %
-                        (SUBJECT, SESSION, REGISTRATION, fname))
+                        (SUBJECT, SESSION, REGISTRATION, base_name))
 
     def test_reconstruction(self):
         logger(__name__).debug("Testing the XNATCopy interface on %s %s"
@@ -110,11 +110,11 @@ def test_reconstruction(self):
             assert_is_not_none(recon_obj,
                         "Upload did not create the %s %s reconstruction: %s" %
                         (SUBJECT, SESSION, RECON))
-            _, fname = os.path.split(FIXTURE)
-            file_obj = recon_obj.out_resource('NIFTI').file(fname)
+            _, base_name = os.path.split(FIXTURE)
+            file_obj = recon_obj.out_resource('NIFTI').file(base_name)
             assert_true(file_obj.exists(),
                         "XNATCopy did not create the %s %s %s file: %s" %
-                        (SUBJECT, SESSION, REGISTRATION, fname))
+                        (SUBJECT, SESSION, REGISTRATION, base_name))
 
     def test_assessor(self):
         logger(__name__).debug("Testing the XNATCopy interface on %s %s"
@@ -134,11 +134,11 @@ def test_assessor(self):
             assert_is_not_none(anl_obj, "XNATCopy did not create the %s %s"
                                         " analysis: %s" %
                                         (SUBJECT, SESSION, ANALYSIS))
-            _, fname = os.path.split(FIXTURE)
-            file_obj = anl_obj.out_resource('params').file(fname)
+            _, base_name = os.path.split(FIXTURE)
+            file_obj = anl_obj.out_resource('params').file(base_name)
             assert_true(file_obj.exists(), "XNATCopy did not create the %s %s"
                                            " %s file: %s" %
-                                           (SUBJECT, SESSION, ANALYSIS, fname))
+                                           (SUBJECT, SESSION, ANALYSIS, base_name))
 
 
 if __name__ == "__main__":