Improve io.smv

ncempy/io/smv.py

@@ -200,9 +200,9 @@ def smvWriter(out_path, dp, camera_length=110, lamda=0.0197, pixel_size=0.01, be
         calibrations of detector distances and beam center. Default is 1.
     newline : str (optional)
         Allow the user to specify the newline character. For data written on Windows computers
-        some microED processing programs in Linux are not able to load SMV files with Windows 
+        some processing programs in Linux are not able to load SMV files with Windows 
         carriage return and newline characters. Use '\n' on Windows machines to enforce Linux
-        line endings. THe defauly None will use the system default.
+        line endings. The default `None` will use the system default.
     """
     if dp.dtype != np.uint16:
         raise TypeError("Only uint16 data type is supported.")
@@ -260,6 +260,11 @@ def smvReader(file_name, verbose=False):
     -------
         out : dict
             A dictionary containing the data and interesting metadata.
+
+    Note
+    ----
+    The returned dictionary has an entry called `pixelSize`. This is the calibrated distance
+    in angstroms. It is not the physical size of a detector pixel. 
 
     Example
     -------
@@ -276,11 +281,10 @@ def smvReader(file_name, verbose=False):
         im1 = f1.getDataset()  # read in the dataset
 
         # Calculate the pixel size in inverse angstroms according to the geometry in the header
-        alpha = f1.header_info['PIXEL_SIZE'] / f1.header_info['DISTANCE'] # angle across 1 pixel
+        BIN = [int(ii) for ii in f1.header_info['BIN'].split('x')]
+        alpha = (BIN[0] * f1.header_info['PIXEL_SIZE']) / f1.header_info['DISTANCE'] # angle across 1 pixel
         dp_pixel_distance = alpha / f1.header_info['WAVELENGTH'] * 1e-10 # divide by wavelength to get distance in Angstroms
         pixelSize = (dp_pixel_distance, dp_pixel_distance)
-        f1.dataOut = {'pixelSize': pixelSize, 'pixelUnit':'A', 'filename': f1.file_name, 
-                        'BIN':f1.header_info['BIN']}
-        print('Warning: pixelSize does not take binning into account.')
-
-    return im1  # return the data and metadata as a dictionary
+        extra_metadata = {'pixelSize': pixelSize, 'pixelUnit':'A', 'filename': f1.file_name}
+    im1.update(extra_metadata)
+    return im1

ncempy/test/test_io_smv.py

@@ -69,3 +69,10 @@ def test_newline_windows(self, temp_file):
             vals = f0.read(3)
             assert vals[1] == ord('\r')
             assert vals[2] == ord('\n')
+
+    def test_smvReader(self, data_location):
+        file_path = data_location / Path('biotin_smv.img')
+        dd = ncempy.io.smv.smvReader(file_path)
+        assert 'data' in dd
+        assert dd['data'].shape[0] == 2048
+