1) fix datatype to uint16 for now; 2) fix bema tilt set from tuple or list; 3) fix thumbnail dims and use 8-bit; 4)tif resolution is a rational number; 5) fix com error parsing

Author: azazellochg

pytemscript/clients/com_client.py

@@ -233,7 +233,9 @@ def handle_com_error(com_error):
         """ Try catching COM error. """
         try:
             error_code = TEMScriptingError(int(com_error.args[0])).name
-            error_msg = com_error.args[2][0].split("]")[-1]
+            error_msg = com_error.args[2][0]
+            if error_msg is not None:
+                error_msg = error_msg.split("]")[-1]
         except (ValueError, IndexError, TypeError):
             error_code = TEMScriptingError.E_NOT_OK.name
             error_msg = str(com_error)

pytemscript/modules/autoloader.py

@@ -59,7 +59,7 @@ def load_cartridge(self, slot: int) -> None:
 
     def unload_cartridge(self) -> None:
         """ Unloads the cartridge currently in the microscope and puts it back into its
-        slot in the cassette.
+        slot in the cassette. Does nothing if no cartridge is on stage.
         """
         if self.is_available:
             body = RequestBody(attr=self.__id + ".UnloadCartridge()")

pytemscript/modules/extras.py

@@ -6,6 +6,7 @@
 from pathlib import Path
 import numpy as np
 from collections import OrderedDict
+from fractions import Fraction
 import PIL.Image as PilImage
 import PIL.TiffImagePlugin as PilTiff
 
@@ -182,8 +183,8 @@ def __create_tiff_tags(self):
             dpcm_width = 1 / (float(pixel_width) * 100)
             dpcm_height = 1 / (float(pixel_height) * 100)
 
-            tiff_tags[PilTiff.X_RESOLUTION] = int(dpcm_width)
-            tiff_tags[PilTiff.Y_RESOLUTION] = int(dpcm_height)
+            tiff_tags[PilTiff.X_RESOLUTION] = Fraction(int(dpcm_width), 1)
+            tiff_tags[PilTiff.Y_RESOLUTION] = Fraction(int(dpcm_height), 1)
 
         # Bit Depth & Color Interpretation
         bit_depth = metadata.get("bit_depth", 16)
@@ -201,7 +202,7 @@ def save(self,
 
         :param fn: Filepath
         :type fn: Path or str
-        :param bool thumbnail: Create a 512px-wide thumbnail, height is adjusted to keep the aspect ratio. Only for non-MRC formats
+        :param bool thumbnail: Create a 512px-wide 8-bit thumbnail, height is adjusted to keep the aspect ratio. Only for non-MRC formats
         :param bool overwrite: Overwrite existing file
         """
         fn = os.path.abspath(fn)
@@ -219,11 +220,12 @@ def save(self,
                 raise FileExistsError("File %s already exists, use overwrite flag" % fn)
 
             logging.getLogger("PIL").setLevel(logging.INFO)
-            pil_image = PilImage.fromarray(self.data.copy(), mode='I;16')
+            data = self.data.copy()
 
             if thumbnail:
-                # create a thumbnail
-                width, height = self.data.shape
+                # create an 8-bit thumbnail
+                pil_image = PilImage.fromarray(data, mode='L')
+                height, width = data.shape
                 if width < height:
                     width = max(round(width * 512 / height), 1)
                     thumbnail_size = (width, 512)
@@ -232,6 +234,8 @@ def save(self,
                     thumbnail_size = (512, height)
 
                 pil_image.thumbnail(size=thumbnail_size, resample=PilImage.Resampling.LANCZOS)
+            else:
+                pil_image = PilImage.fromarray(data, mode='I;16')
 
             # create tiff tags
             if ext in [".tif", ".tiff"] and not thumbnail:

pytemscript/modules/illumination.py

@@ -279,14 +279,14 @@ def beam_tilt(self) -> Union[Vector, float]:
             return Vector(0.0, 0.0)  # Microscope might return nonsense if DFMode is OFF
 
     @beam_tilt.setter
-    def beam_tilt(self, tilt: Union[Vector, float]) -> None:
+    def beam_tilt(self, tilt: Union[Vector, float, List[float], Tuple[float, float]]) -> None:
         body = RequestBody(attr=self.__id + ".DFMode", validator=int)
         mode = self.__client.call(method="get", body=body)
 
         if isinstance(tilt, float):
             tilt = Vector(tilt, tilt)
 
-        tilt *= 1e-3 # mrad to rad
+        tilt = Vector.convert_to(tilt) * 1e-3 # mrad to rad
 
         if tilt == (0.0, 0.0):
             body = RequestBody(attr=self.__id + ".Tilt", value=tilt)

pytemscript/utils/misc.py

@@ -60,9 +60,10 @@ def send_data(sock, data: bytes, datatype="msg") -> None:
     :param str datatype: data type
 
     The packet includes the following:
-        - type: 2 bytes
+        - header: 2 bytes
         - length of data: 4 bytes
-        - checksum: 20 bytes - only if type is "data"
+        - checksum: 20 bytes - only if header == HEADER_DATA
+        - actual data
     """
     packet = bytearray()
     packet.extend(HEADER_MSG if datatype == "msg" else HEADER_DATA)
@@ -163,16 +164,16 @@ def convert_image(obj,
     metadata = {
         "width": width or int(obj.Width),
         "height": height or int(obj.Height),
-        "bit_depth": int(bit_depth or (obj.BitDepth if advanced else obj.Depth)),
-        "pixel_type": ImagePixelType(obj.PixelType).name if advanced else ImagePixelType.SIGNED_INT.name,
+        "bit_depth": 16, # int(bit_depth or (obj.BitDepth if advanced else obj.Depth)),
+        "pixel_type": ImagePixelType.UNSIGNED_INT.name # ImagePixelType(obj.PixelType).name if advanced
     }
     if pixel_size is not None:
         metadata["PixelSize.Width"] = pixel_size
         metadata["PixelSize.Height"] = pixel_size
     if advanced:
         metadata.update({item.Key: item.ValueAsString for item in obj.Metadata})
-    if "BitsPerPixel" in metadata:
-        metadata["bit_depth"] = int(metadata["BitsPerPixel"])
+    #if "BitsPerPixel" in metadata:
+    #    metadata["bit_depth"] = int(metadata["BitsPerPixel"])
 
     return Image(data, name, metadata)