Merge 48ae501 into 5a9d0fe

nanonispy/read.py

@@ -115,6 +115,9 @@ def start_byte(self):
 
             for line in f:
                 # Convert from bytes to str
+                #entry = line.strip().decode()
+                entry = line.strip().decode('utf-8', 'ignore')
+
                 try:
                     entry = line.strip().decode()
                 except UnicodeDecodeError:
@@ -225,9 +228,15 @@ def _load_data(self):
 
         # pixel size in bytes
         exp_size_per_pix = num_param + num_sweep*num_chan
+
+        ## pad griddata if incomplete
+        if len(griddata) < nx * ny * exp_size_per_pix:
+            paddiff = nx * ny * exp_size_per_pix - len(griddata)
+            griddata = np.pad(griddata, (0, paddiff), 'constant')
 
         # reshape from 1d to 3d
-        griddata_shaped = griddata.reshape((nx, ny, exp_size_per_pix))
+        # griddata_shaped = griddata.reshape((nx, ny, exp_size_per_pix))
+        griddata_shaped = griddata.reshape((ny, nx, exp_size_per_pix))
 
         # experimental parameters are first num_param of every pixel
         params = griddata_shaped[:, :, :num_param]
@@ -357,7 +366,8 @@ def _load_data(self):
         f.close()
 
         # reshape
-        scandata_shaped = scandata.reshape(nchanns, ndir, nx, ny)
+#        scandata_shaped = scandata.reshape(nchanns, ndir, nx, ny)
+        scandata_shaped = scandata.reshape(nchanns, ndir, ny, nx)
 
         # extract data for each channel
         for i, chann in enumerate(channs):
@@ -418,9 +428,11 @@ def _load_data(self):
 
         column_names = f.readline().strip('\n').split('\t')
         f.close()
+
         num_lines = self._num_header_lines()
         specdata = np.genfromtxt(self.fname, delimiter='\t', skip_header=num_lines)
 
+
         for i, name in enumerate(column_names):
             data_dict[name] = specdata[:, i]
 
@@ -473,6 +485,7 @@ def _parse_3ds_header(header_raw, header_override):
     header_entries = header_raw.split('\r\n')
     header_entries = header_entries[:-2]
 
+
     # Convert the strings to a dictionary.
     raw_dict = dict()
     for entry in header_entries:
@@ -679,6 +692,7 @@ def _split_header_entry(entry):
     those by ';' character.
     """
 
+
     key_str, val_str = entry.split("=", 1)
 
     if ';' in val_str:
@@ -687,6 +701,7 @@ def _split_header_entry(entry):
         return key_str, val_str.strip('"')
 
 
+
 def save_array(file, arr, allow_pickle=True):
     """
     Wrapper to numpy.save method for arrays.