3.0b2

docs/components/index.rst

@@ -21,7 +21,7 @@ Relative to TEM V1.9 standard scripting adapter:
     * Camera
     * Configuration
     * Gun
-    * Gun1 (untested)
+    * Gun1
     * Illumination
     * InstrumentModeControl
     * Projection
@@ -34,10 +34,10 @@ Relative to TEM V1.2 advanced scripting adapter:
 
     * Acquisitions
     * Autoloader
-    * EnergyFilter (untested)
+    * EnergyFilter
     * Phaseplate
     * PiezoStage (untested)
-    * Source (untested)
+    * Source
     * TemperatureControl
     * UserDoorHatch (untested)
 

docs/installation.rst

@@ -60,13 +60,13 @@ Latest supported Python version on Windows XP is 3.4. Download pytemscript and i
 
 .. code-block:: python
 
-    pip download -d . pytemscript --python-version 34 --only-binary=:all: --platform win32
+    pip download -d . pytemscript comtypes==1.2.1 mrcfile==1.3.0 numpy==1.15.4 pillow==5.3.0 typing --python-version 34 --only-binary=:all: --platform win32
 
 Copy downloaded \*.whl files to the target PC and install them:
 
 .. code-block:: python
 
-    py -m pip install pytemscript --no-index --find-links .
+    py -m pip install pytemscript typing --no-index --find-links .
 
 Testing
 -------

docs/remote.rst

@@ -42,6 +42,8 @@ Then you can connect to the server as shown below:
 
 Diagnostic messages are saved to ``socket_client.log`` and ``socket_server.log`` as well as printed to the console. Log files are rotated weekly at midnight.
 
+To shutdown pytemscript-server, press Ctrl+C in the console.
+
 UTAPI client
 ------------
 
@@ -53,8 +55,7 @@ you can search for ``utapi_server.exe`` in the Task Manager. The server is liste
 **46699**. Under the hood UTAPI utilizes gRPC (Google Remote Procedure Calls) framework that uses protocol
 buffers for communication.
 
-Here we provide a Python client that converts API commands to UTAPI calls.
-The client requires extra dependencies to be installed:
+Pytemscript converts its API commands to UTAPI calls. The client requires extra dependencies to be installed:
 
 .. code-block:: python
 

pyproject.toml.future

@@ -36,7 +36,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-extra = ["matplotlib", "mypy"]
+dev = ["matplotlib", "mypy"]
 utapi = ["grpcio", "grpcio-tools", "protobuf"]
 
 [project.urls]

pytemscript/__init__.py

@@ -1 +1 @@
-__version__ = '3.0b1'
+__version__ = '3.0b2'

pytemscript/clients/base_client.py

@@ -20,6 +20,11 @@ def has_lowdose_iface(self) -> bool:
     def has_ccd_iface(self) -> bool:
         raise NotImplementedError("Method must be implemented in subclass")
 
+    @property
+    @lru_cache(maxsize=1)
+    def has_calgetter_iface(self) -> bool:
+        raise NotImplementedError("Method must be implemented in subclass")
+
     def call(self, method: str, body: RequestBody):
         """ Main method used by modules. """
         raise NotImplementedError("Method must be implemented in subclass")

pytemscript/clients/com_client.py

@@ -24,6 +24,7 @@ def __init__(self,
         self.tem_adv = None
         self.tem_lowdose = None
         self.tecnai_ccd = None
+        self.calgetter = None
 
         if platform.system() == "Windows":
             logging.getLogger("comtypes").setLevel(logging.INFO)
@@ -64,6 +65,8 @@ def _initialize(self, useLD: bool, useTecnaiCCD: bool):
             if self.tecnai_ccd is None:
                 self.tecnai_ccd = self._createCOMObject(SCRIPTING_TECNAI_CCD2)
 
+        self.calgetter = self._createCOMObject(CALGETTER)
+
         if self.tem is None:
             raise RuntimeError("Failed to create COM object.")
 
@@ -73,6 +76,7 @@ def _close(self):
         self.tem_adv = None
         self.tem_lowdose = None
         self.tecnai_ccd = None
+        self.calgetter = None
 
         com_module.CoUninitialize()
 
@@ -124,6 +128,11 @@ def has_lowdose_iface(self) -> bool:
     def has_ccd_iface(self) -> bool:
         return self._scope.tecnai_ccd is not None
 
+    @property
+    @lru_cache(maxsize=1)
+    def has_calgetter_iface(self) -> bool:
+        return self._scope.calgetter is not None
+
     def _get(self, attrname):
         return rgetattr(self._scope, attrname)
 
@@ -163,6 +172,9 @@ def _exec_special(self, attrname, **kwargs):
         if obj_cls is None or obj_method is None:
             raise AttributeError("obj_class and obj_method must be specified")
 
+        logging.debug("=> EXEC_SP: %s.%s, kwargs=%r",obj_cls.__name__,
+                      obj_method, kwargs)
+
         if attrname is None:  # plugin case
             com_obj = self._scope
         else:
@@ -171,7 +183,7 @@ def _exec_special(self, attrname, **kwargs):
         method = getattr(obj_instance, obj_method)
 
         if method is None:
-            raise AttributeError("Method %s not implemented for %s" % (obj_method, obj_cls))
+            raise AttributeError("Method %s not implemented for %s" % (obj_method, obj_cls.__name__))
 
         result = method(**kwargs)
 

pytemscript/clients/socket_client.py

@@ -66,6 +66,14 @@ def has_ccd_iface(self) -> bool:
 
         return response
 
+    @property
+    @lru_cache(maxsize=1)
+    def has_calgetter_iface(self) -> bool:
+        response = self.__send_request({"method": "has_calgetter_iface"})
+        logging.debug("Received response: %s", response)
+
+        return response
+
     def call(self, method: str, body: RequestBody):
         """ Main method used by modules. """
         payload = {"method": method, "body": body}

pytemscript/modules/acquisition.py

@@ -109,7 +109,7 @@ def show_cameras_cca(self, tem_cameras: Dict) -> Dict:
 
         return tem_cameras
 
-    def acquire(self, cameraName: str) -> Image:
+    def acquire(self, cameraName: str, **kwargs) -> Image:
         """ Perform actual acquisition. Camera settings should be set beforehand.
 
         :param cameraName: Camera name
@@ -121,7 +121,7 @@ def acquire(self, cameraName: str) -> Image:
         t0 = time.time()
         imgs = acq.AcquireImages()
         t1 = time.time()
-        image = convert_image(imgs[0], name=cameraName)
+        image = convert_image(imgs[0], name=cameraName, **kwargs)
         t2 = time.time()
         logging.debug("\tAcquisition took %f s" % (t1 - t0))
         logging.debug("\tConverting image took %f s" %(t2 - t1))
@@ -130,7 +130,8 @@ def acquire(self, cameraName: str) -> Image:
 
     def acquire_advanced(self,
                          cameraName: str,
-                         recording: bool = False) -> Optional[Image]:
+                         recording: bool = False,
+                         **kwargs) -> Optional[Image]:
         """ Perform actual acquisition with advanced scripting. """
         if recording:
             self.com_object.CameraContinuousAcquisition.Start()
@@ -141,7 +142,7 @@ def acquire_advanced(self,
             img = self.com_object.CameraSingleAcquisition.Acquire()
             t1 = time.time()
             #self.com_object.CameraSingleAcquisition.Wait()
-            image = convert_image(img, name=cameraName, advanced=True)
+            image = convert_image(img, name=cameraName, advanced=True, **kwargs)
             t2 = time.time()
             logging.debug("\tAcquisition took %f s" % (t1 - t0))
             logging.debug("\tConverting image took %f s" % (t2 - t1))
@@ -270,39 +271,52 @@ def set_tem_presets_advanced(self,
             else:
                 raise NotImplementedError("This camera does not support electron counting")
 
-        if eer is not None and hasattr(capabilities, 'SupportsEER'):
-            if capabilities.SupportsEER:
+        # EER saving is supported in TEM server 7.6 (Titan 3.6 / Talos 2.6)
+        if hasattr(capabilities, 'SupportsEER'):
+            eer_is_supported = capabilities.SupportsEER
+            if eer and eer_is_supported:
                 settings.EER = eer
-                if eer and not settings.ElectronCounting:
-                    raise RuntimeError("Electron counting should be enabled when using EER")
-                if eer and 'group_frames' in kwargs:
-                    raise RuntimeError("No frame grouping allowed when using EER")
-            else:
+            elif eer and not eer_is_supported:
                 raise NotImplementedError("This camera does not support EER")
+            elif not eer and eer_is_supported:
+                # EER param is persistent throughout camera COM object lifetime,
+                # if not using EER we need to set it to False
+                settings.EER = False
+
+            if eer and not settings.ElectronCounting:
+                raise RuntimeError("Electron counting should be enabled when using EER")
+            if eer and 'group_frames' in kwargs:
+                raise RuntimeError("No frame grouping allowed when using EER")
+
+        if capabilities.SupportsDoseFractions:
+            dfd = settings.DoseFractionsDefinition
+            dfd.Clear()
+
+        if kwargs.get('save_frames'):
+            if not capabilities.SupportsDoseFractions:
+                raise NotImplementedError("This camera does not support dose fractions")
 
-        if 'save_frames' in kwargs:
             total = settings.CalculateNumberOfFrames()
             now = datetime.now()
             settings.SubPathPattern = cameraName + "_" + now.strftime("%d%m%Y_%H%M%S")
             output = settings.PathToImageStorage + settings.SubPathPattern
 
-            if eer is None:
+            if eer in [False, None]:
                 group = kwargs.get('group_frames', 1)
                 if group < 1:
                     raise ValueError("Frame group size must be at least 1")
                 if group > total:
                     raise ValueError("Frame group size cannot exceed maximum possible "
                                      "number of frames: %d. Change exposure time." % total)
 
-                dfd = settings.DoseFractionsDefinition
-                dfd.Clear()
                 frame_ranges = [(i, min(i + group, total)) for i in range(0, total-1, group)]
-                for i in frame_ranges:
+                logging.debug("Using frame ranges: %s", frame_ranges[:-1])
+                for i in frame_ranges[:-1]:
                     dfd.AddRange(i[0], i[1])
 
                 logging.info("Movie of %d fractions (%d frames, group=%d) "
                              "will be saved to: %s.mrc",
-                             len(frame_ranges), total, group, output)
+                             len(frame_ranges)-1, total, group, output)
                 logging.info("MRC format can only contain images of up to "
                              "16-bits per pixel, to get true CameraCounts "
                              "multiply pixels by PixelToValueCameraCounts "
@@ -431,7 +445,7 @@ def __acquire_with_tecnaiccd(self,
                                "pass useTecnaiCCD=True to the Microscope() ?")
         else:
             logging.info("Using TecnaiCCD plugin for Gatan camera")
-            from ..plugins.tecnai_ccd_plugin import TecnaiCCDPlugin
+            from ..plugins.tecnai_ccd import TecnaiCCDPlugin
 
             body = RequestBody(attr=None,
                                obj_cls=TecnaiCCDPlugin,
@@ -506,7 +520,8 @@ def acquire_tem_image(self,
             body = RequestBody(attr="tem.Acquisition",
                                obj_cls=AcquisitionObj,
                                obj_method="acquire",
-                               cameraName=cameraName)
+                               cameraName=cameraName,
+                               **kwargs)
             image = self.__client.call(method="exec_special", body=body)
             logging.info("TEM image acquired on %s", cameraName)
 
@@ -537,7 +552,8 @@ def acquire_tem_image(self,
                                    obj_cls=AcquisitionObj,
                                    obj_method="acquire_advanced",
                                    cameraName=cameraName,
-                                   recording=kwargs["recording"])
+                                   recording=kwargs["recording"],
+                                   **kwargs)
                 self.__client.call(method="exec_special", body=body)
                 logging.info("TEM image acquired on %s", cameraName)
                 return None
@@ -546,7 +562,8 @@ def acquire_tem_image(self,
                                    validator=Image,
                                    obj_cls=AcquisitionObj,
                                    obj_method="acquire_advanced",
-                                   cameraName=cameraName)
+                                   cameraName=cameraName,
+                                   **kwargs)
                 image = self.__client.call(method="exec_special", body=body)
                 return image
 
@@ -587,7 +604,8 @@ def acquire_stem_image(self,
                            validator=Image,
                            obj_cls=AcquisitionObj,
                            obj_method="acquire",
-                           cameraName=cameraName)
+                           cameraName=cameraName,
+                           **kwargs)
         image = self.__client.call(method="exec_special", body=body)
         logging.info("STEM image acquired on %s", cameraName)
 

pytemscript/modules/autoloader.py

@@ -13,7 +13,7 @@ def __init__(self, client):
         self.__id = "tem.AutoLoader"
         self.__id_adv = "tem_adv.AutoLoader"
         self.__err_msg = "Autoloader is not available"
-        self.__err_msg_adv = "This function is not available in your advanced scripting interface."
+        self.__err_msg_adv = "Autoloader advanced interface is not available. Requires TEM server 7.8+"
 
     @property
     @lru_cache(maxsize=1)

pytemscript/modules/energyfilter.py

@@ -10,7 +10,7 @@ class EnergyFilter:
     def __init__(self, client):
         self.__client = client
         self.__id = "tem_adv.EnergyFilter"
-        self.__err_msg = "EnergyFilter interface is not available"
+        self.__err_msg = "EnergyFilter advanced interface is not available. Requires TEM server 7.8+"
 
     @property
     @lru_cache(maxsize=1)

pytemscript/modules/extras.py

@@ -45,7 +45,7 @@ def __init__(self, x: float, y: float) -> None:
         self.__min = None
         self.__max = None
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         return "Vector(x=%f, y=%f)" % (self.x, self.y)
 
     def __str__(self):
@@ -150,6 +150,9 @@ def __init__(self,
         else:
             self.timestamp = datetime.now().strftime("%Y:%m:%d %H:%M:%S")
 
+    def __repr__(self) -> str:
+        return "Image()"
+
     @lru_cache(maxsize=1)
     def __create_tiff_tags(self):
         """Create TIFF tags from metadata. """
@@ -229,6 +232,9 @@ class SpecialObj:
     def __init__(self, com_object):
         self.com_object = com_object
 
+    def __repr__(self):
+        return "%s()" % self.__class__.__name__
+
 
 class StageObj(SpecialObj):
     """ Wrapper around stage / piezo stage COM object. """