temscript 2.0.1__tar.gz → 2.2.0__tar.gz

{temscript-2.0.1/temscript.egg-info → temscript-2.2.0}/PKG-INFO

@@ -1,7 +1,7 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: temscript
-Version: 2.0.1
-Summary: TEM Scripting adapter for FEI microscopes
+Version: 2.2.0
+Summary: TEM Scripting adapter for TFS/FEI transmission electron microscopes
 Home-page: https://github.com/niermann/temscript
 Author: Tore Niermann
 Author-email: tore.niermann@tu-berlin.de
@@ -21,6 +21,20 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.4
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: numpy
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # About
 

{temscript-2.0.1 → temscript-2.2.0}/docs/changelog.rst

@@ -1,6 +1,28 @@
 Changelog
 =========
 
+Version 2.2.0
+^^^^^^^^^^^^^
+
+* Added get_instrument_id(), which returns the microscope's serial number (D-number, without "D" prefix) from the
+  Windows registry (or an empty string if unavailable).
+* Added get_computer_name(), which returns the hostname of the microscope computer.
+* Deprecated get_microscope_id() as the term is ambiguous, use get_computer_name() or get_instrument_id() instead.
+* Added "instrument_id" and "computer_name" entries to the dictionary returned by get_state(). The "microscope_id"
+  entry is deprecated and will be removed in future versions.
+
+Version 2.1.1
+^^^^^^^^^^^^^
+
+* Fixed error handling in server
+* Don't throw error for get_stage_holder(), if no holder inserted
+
+Version 2.1.0
+^^^^^^^^^^^^^
+
+* Changed default apartment model to COINIT_APARTMENTTHREADED to increase compatibility with comtypes
+* COM initialization respects setting from sys.coinit_flags
+
 Version 2.0.1
 ^^^^^^^^^^^^^
 

{temscript-2.0.1 → temscript-2.2.0}/docs/conf.py

@@ -125,7 +125,7 @@ html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+#html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.

{temscript-2.0.1 → temscript-2.2.0}/docs/instrument.rst

@@ -13,6 +13,13 @@ The interface is described in detail in the scripting manual of your microscope
 The manual is your ultimate reference, this documentation will only describe the
 python wrapper to the COM interface.
 
+The COM apartment model will automatically be initialized as ``COINIT_APARTMENTTHREADED``
+(this changed in Version 2.1.0, it was ``COINIT_MULTITHREADED`` before). However, if the
+apartment model was already initialized as ``COINIT_MULTITHREADED`` before `temscript`
+was imported, `temscript` will also work. If you want a specific apartment model, set the
+variable ``sys.coinit_flags`` before importing `temscript`.
+
+
 Enumerations
 ^^^^^^^^^^^^
 

{temscript-2.0.1 → temscript-2.2.0}/docs/restrictions.rst

@@ -8,6 +8,10 @@ to this scripting interface, thus these issues also occur using `temscript`. As
 with the scripting interfaces by FEI or Thermo Fisher Scientific themself, known issues are listed here for the user's
 reference.
 
+* The standard scripting interface does not expose the microscope's serial number (D-number).
+  ``get_instrument_id()`` reads the ``Instrument Key`` DWORD from ``HKEY_LOCAL_MACHINE\SOFTWARE\FEI\Configuration``
+  instead (verified on Titan 1.1), returning the number as decimal string without "D" prefix. If the value is
+  missing, inaccessible, not a DWORD, or zero, an empty string is returned.
 * Changing the projection mode from IMAGING to DIFFRACTION and back again changes the magnification in imaging
   mode (Titan 1.1).
 * :attr:`Projection.Magnification` does not return the actual magnification, but always 0.0 (Titan 1.1)

temscript-2.2.0/scripts/test_com.py

@@ -0,0 +1,34 @@
+from temscript._com import CLSCTX_ALL, IUnknown, co_create_instance
+from temscript._instrument_com import LongProperty, ObjectProperty
+from uuid import UUID
+
+# This test requires the TemscriptMockObject.dll to be registered
+# Use "regsvr32.exe TemscriptMockObject.dll" with admin privileges to register it, before running this script
+CLSID_MockObject = UUID('e5766dfa-303e-48a9-983e-352fa4a5a408')
+
+class IChildObject(IUnknown):
+    IID = UUID('bbbd2968-4b93-49a9-b1ae-16d1d6b563eb')
+
+    value = LongProperty(get_index=3, put_index=4)
+
+
+class IMockObject(IUnknown):
+    IID = UUID('bbbd2968-4b93-49a9-b1ae-16d1d6b563eb')
+
+    value = LongProperty(get_index=3, put_index=4)
+    child = ObjectProperty(IChildObject, get_index=5)
+
+
+def test_mock_object():
+    obj = co_create_instance(CLSID_MockObject, CLSCTX_ALL, IMockObject)
+
+    obj.value = 123
+    assert obj.value == 123
+
+    child = obj.child
+    child.value = 321
+    assert child.value == 321
+    assert obj.value == 123
+
+
+test_mock_object()

{temscript-2.0.1 → temscript-2.2.0}/scripts/test_microscope.py

@@ -31,6 +31,8 @@ else:
 
 print("Microscope.get_family():", microscope.get_family())
 print("Microscope.get_microscope_id():", microscope.get_microscope_id())
+print("Microscope.get_computer_name():", microscope.get_computer_name())
+print("Microscope.get_instrument_id():", microscope.get_instrument_id())
 print("Microscope.get_version():", microscope.get_version())
 print("Microscope.get_voltage():", microscope.get_voltage())
 print("Microscope.get_vacuum():", microscope.get_vacuum())

{temscript-2.0.1 → temscript-2.2.0}/setup.py

@@ -14,7 +14,7 @@ with open("temscript/version.py") as fp:
 
 setup(name='temscript',
     version=__version__,
-    description='TEM Scripting adapter for FEI microscopes',
+    description='TEM Scripting adapter for TFS/FEI transmission electron microscopes',
     author='Tore Niermann',
     author_email='tore.niermann@tu-berlin.de',
     long_description=long_description,

{temscript-2.0.1 → temscript-2.2.0}/temscript/_com.py

@@ -6,6 +6,7 @@ __all__ = 'UUID', 'CLSCTX_ALL', 'IUnknown', 'co_create_instance', 'SafeArray', '
 
 # COM constants
 COINIT_MULTITHREADED = 0
+COINIT_APARTMENTTHREADED = 2
 CLSCTX_ALL = 0x17
 
 
@@ -370,5 +371,27 @@ class SafeArray:
 
 
 _ole32 = ctypes.oledll.ole32
-_ole32.CoInitializeEx(None, ctypes.c_int(COINIT_MULTITHREADED))
 _oleauto = ctypes.windll.oleaut32
+
+def initialize_com(flags=None):
+    RPC_E_CHANGED_MODE = -2147417850
+
+    # The comtypes package allows to specify the apartment model by
+    # setting sys.coinit_flags in advance. We copy this behavior.
+    if flags is None:
+        import sys
+        flags = getattr(sys, "coinit_flags", None)
+
+    if flags is None:
+        # If we don't have explicit flags, try STA first and fall back to MTA
+        # if COM is already initialized to MTA.
+        try:
+            _ole32.CoInitializeEx(None, ctypes.c_int(COINIT_APARTMENTTHREADED))
+        except WindowsError as exc:
+            if exc.winerror == RPC_E_CHANGED_MODE:
+                _ole32.CoInitializeEx(None, ctypes.c_int(COINIT_MULTITHREADED))
+    else:
+        # Otherwise, use the apartment model we got
+        _ole32.CoInitializeEx(None, flags)
+
+initialize_com()

{temscript-2.0.1 → temscript-2.2.0}/temscript/_instrument_com.py

@@ -28,7 +28,7 @@ class LongProperty(BaseProperty):
         if self._get_index is None:
             raise AttributeError("Attribute %s is not readable" % self._name)
         result = ctypes.c_long(-1)
-        prototype = ctypes.WINFUNCTYPE(ctypes.HRESULT, ctypes.c_void_p)(self._get_index, "get_property")
+        prototype = ctypes.WINFUNCTYPE(ctypes.HRESULT, ctypes.POINTER(ctypes.c_long))(self._get_index, "get_property")
         prototype(obj.get(), ctypes.byref(result))
         return result.value
 

{temscript-2.0.1 → temscript-2.2.0}/temscript/base_microscope.py

@@ -84,14 +84,48 @@ class BaseMicroscope(ABC):
         """Return product family (see :class:`ProductFamily` for values): "TITAN", "TECNAI", ..."""
         raise NotImplementedError
 
-    @abstractmethod
     def get_microscope_id(self):
         """
-        Return microscope ID.
+        Return hostname of microscope's computer.
 
-        There is no way to read this via the scripting adapter directly, thus this method uses hostname instead.
+        .. deprecated:: 2.2.0
+            The term "microscope ID" is ambiguous. FEI/TFS instruments identify themselves by the computer name
+            and the instrument ID (as also stored in Velox metadata), use :meth:`get_computer_name` or
+            :meth:`get_instrument_id` instead.
         """
-        raise NotImplementedError
+        import warnings
+        warnings.warn("Microscope.get_microscope_id() is deprecated. "
+                      "Use get_computer_name() and/or get_instrument_id() instead.",
+                      category=DeprecationWarning, stacklevel=2)
+        return self.get_computer_name()
+
+    def get_computer_name(self):
+        """
+        Return name (hostname) of the microscope computer.
+
+        This corresponds to the computer name stored by FEI/TFS software, e.g. in Velox metadata.
+
+        .. versionadded:: 2.2.0
+        """
+        import socket
+        return socket.gethostname()
+
+    def get_instrument_id(self):
+        """
+        Return serial number of the microscope as string of decimal digits (without the "D" prefix,
+        e.g. "1234" for D1234).
+
+        :class:`Microscope` reads the ``Instrument Key`` DWORD from
+        ``HKEY_LOCAL_MACHINE\\SOFTWARE\\FEI\\Configuration`` in the Windows registry. If the serial number
+        is not available, an empty string is returned. See :ref:`restrictions` for details.
+
+        This corresponds to the instrument ID stored by FEI/TFS software, e.g. in Velox metadata.
+
+        The default implementation returns an empty string.
+
+        .. versionadded:: 2.2.0
+        """
+        return ""
 
     @abstractmethod
     def get_version(self):
@@ -641,7 +675,11 @@ class BaseMicroscope(ABC):
     def get_indicated_camera_length(self):
         """
         Return (indicated) camera length in meters in diffraction modes.
-        If microscope is in imaging mode, 0 is returned.
+
+        .. note::
+            The scripting manual states, that this function always returns 0,
+            if microscope is in imaging mode. In STEM mode this
+            function works reportedly nevertheless.
 
         .. versionadded:: 1.0.9
         """
@@ -651,7 +689,11 @@ class BaseMicroscope(ABC):
     def get_indicated_magnification(self):
         """
         Return (indicated) magnification in imaging modes.
-        If microscope is in diffraction mode, 0 is returned.
+
+        .. note::
+            The scripting manual states, that this function always returns 0,
+            if microscope is in diffraction mode. In STEM mode this
+            function works reportedly nevertheless.
 
         .. note::
             On Titan 1.1 software this method returns 0.0 regardless of used mode. See :ref:`restrictions`.
@@ -1123,10 +1165,19 @@ class BaseMicroscope(ABC):
 
         .. versionchanged:: 2.0
             The method was renamed from get_optics_state() to get_state()
+
+        .. versionchanged:: 2.2.0
+            Added "instrument_id" and "computer_name" entries.
+
+        .. deprecated:: 2.2.0
+            The "microscope_id" entry is deprecated and will be removed in future versions. It contains the
+            same value as "computer_name", use that entry instead. See :meth:`get_microscope_id`.
         """
         state = {
             "family": self.get_family(),
-            "microscope_id": self.get_microscope_id(),
+            "microscope_id": self.get_computer_name(),
+            "instrument_id": self.get_instrument_id(),
+            "computer_name": self.get_computer_name(),
             "temscript_version": self.get_version(),
             "voltage(kV)": self.get_voltage(),
             "stage_holder": self.get_stage_holder(),
@@ -1174,5 +1225,6 @@ class BaseMicroscope(ABC):
             use :meth:`get_state` instead.
         """
         import warnings
-        warnings.warn("Microscope.get_optics_state() is deprecated. Use get_state() instead.", DeprecationWarning)
+        warnings.warn("Microscope.get_optics_state() is deprecated. Use get_state() instead.",
+                      category=DeprecationWarning, stacklevel=2)
         return self.get_state()

{temscript-2.0.1 → temscript-2.2.0}/temscript/microscope.py

@@ -1,3 +1,4 @@
+import functools
 import math
 
 from temscript.base_microscope import set_enum_attr_from_dict, set_attr_from_dict
@@ -7,6 +8,27 @@ from .instrument import CCDCamera, GetInstrument, STEMDetector
 from .enums import *
 
 
+# Computer name and instrument ID are properties of the machine, thus cached at module level
+# (and not per instance, which would keep instances alive).
+@functools.lru_cache(maxsize=None)
+def _get_computer_name():
+    import socket
+    return socket.gethostname()
+
+
+@functools.lru_cache(maxsize=None)
+def _get_instrument_id():
+    import winreg
+    try:
+        with winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, r"SOFTWARE\FEI\Configuration") as key:
+            value, value_type = winreg.QueryValueEx(key, "Instrument Key")
+        if value_type == winreg.REG_DWORD and value > 0:
+            return str(value)
+    except OSError:
+        pass  # Missing key/value or access denied.
+    return ""
+
+
 class Microscope(BaseMicroscope):
     """
     Hich level interface to local microscope.
@@ -38,9 +60,11 @@ class Microscope(BaseMicroscope):
     def get_family(self):
         return ProductFamily(self._family).name
 
-    def get_microscope_id(self):
-        import socket
-        return socket.gethostname()
+    def get_computer_name(self):
+        return _get_computer_name()
+
+    def get_instrument_id(self):
+        return _get_instrument_id()
 
     def get_version(self):
         from .version import __version__
@@ -79,7 +103,10 @@ class Microscope(BaseMicroscope):
         self._tem_vacuum.ColumnValvesOpen = state
 
     def get_stage_holder(self):
-        return self._tem_stage.Holder.name
+        try:
+            return self._tem_stage.Holder.name
+        except OSError:
+            return ""
 
     def get_stage_status(self):
         return self._tem_stage.Status.name

{temscript-2.0.1 → temscript-2.2.0}/temscript/null_microscope.py

@@ -122,10 +122,6 @@ class NullMicroscope(BaseMicroscope):
     def get_family(self):
         return "NULL"
 
-    def get_microscope_id(self):
-        import socket
-        return socket.gethostname()
-
     def get_version(self):
         from .version import __version__
         return __version__

{temscript-2.0.1 → temscript-2.2.0}/temscript/remote_microscope.py

@@ -130,8 +130,11 @@ class RemoteMicroscope(BaseMicroscope):
     def get_family(self):
         return self._request("GET", "/v1/family")[1]
 
-    def get_microscope_id(self):
-        return self._request("GET", "/v1/microscope_id")[1]
+    def get_computer_name(self):
+        return self._request("GET", "/v1/computer_name")[1]
+
+    def get_instrument_id(self):
+        return self._request("GET", "/v1/instrument_id")[1]
 
     def get_version(self):
         return self._request("GET", "/v1/version")[1]

{temscript-2.0.1 → temscript-2.2.0}/temscript/server.py

@@ -8,15 +8,15 @@ from .marshall import ExtendedJsonEncoder, gzip_encode, MIME_TYPE_PICKLE, MIME_T
 
 
 class MicroscopeHandler(BaseHTTPRequestHandler):
-    GET_V1_FORWARD = ("family", "microscope_id", "version", "voltage", "vacuum", "stage_holder",
-                      "stage_status", "stage_position", "stage_limits", "detectors", "cameras", "stem_detectors",
-                      "stem_acquisition_param", "image_shift", "beam_shift", "beam_tilt", "projection_sub_mode",
-                      "projection_mode", "projection_mode_string", "magnification_index", "indicated_camera_length",
-                      "indicated_magnification", "defocus", "objective_excitation", "intensity", "objective_stigmator",
-                      "condenser_stigmator", "diffraction_shift", "screen_current", "screen_position",
-                      "illumination_mode", "condenser_mode", "illuminated_area", "probe_defocus", "convergence_angle",
-                      "stem_magnification", "stem_rotation", "spot_size_index", "dark_field_mode", "beam_blanked",
-                      "instrument_mode", 'optics_state', 'state', 'column_valves_open')
+    GET_V1_FORWARD = ("family", "microscope_id", "instrument_id", "computer_name", "version", "voltage", "vacuum",
+                      "stage_holder", "stage_status", "stage_position", "stage_limits", "detectors", "cameras",
+                      "stem_detectors", "stem_acquisition_param", "image_shift", "beam_shift", "beam_tilt",
+                      "projection_sub_mode", "projection_mode", "projection_mode_string", "magnification_index",
+                      "indicated_camera_length", "indicated_magnification", "defocus", "objective_excitation",
+                      "intensity", "objective_stigmator", "condenser_stigmator", "diffraction_shift", "screen_current",
+                      "screen_position", "illumination_mode", "condenser_mode", "illuminated_area", "probe_defocus",
+                      "convergence_angle", "stem_magnification", "stem_rotation", "spot_size_index", "dark_field_mode",
+                      "beam_blanked", "instrument_mode", 'optics_state', 'state', 'column_valves_open')
 
     PUT_V1_FORWARD = ("image_shift", "beam_shift", "beam_tilt", "projection_mode", "magnification_index",
                       "defocus", "intensity", "diffraction_shift", "objective_stigmator", "condenser_stigmator",
@@ -58,7 +58,7 @@ class MicroscopeHandler(BaseHTTPRequestHandler):
             else:
                 content_encoding = None
         except Exception as exc:
-            self.log_error("Exception raised during encoding of response: %s" % repr(exc))
+            self.log_error("Exception raised during encoding of response: %s", repr(exc))
             self.send_error(500, "Error handling request '%s': %s" % (self.path, str(exc)))
         else:
             self.send_response(200)
@@ -146,10 +146,10 @@ class MicroscopeHandler(BaseHTTPRequestHandler):
             else:
                 raise KeyError('Unknown API version: %s' % self.path)
         except KeyError as exc:
-            self.log_error("KeyError raised during handling of GET request '%s': %s" % (self.path, repr(exc)))
+            self.log_error("KeyError raised during handling of GET request '%s': %s", self.path, repr(exc))
             self.send_error(404, str(exc))
         except Exception as exc:
-            self.log_error("Exception raised during handling of GET request '%s': %s" % (self.path, repr(exc)))
+            self.log_error("Exception raised during handling of GET request '%s': %s", self.path, repr(exc))
             self.send_error(500, "Error handling request '%s': %s" % (self.path, str(exc)))
         else:
             self.build_response(response)
@@ -163,10 +163,10 @@ class MicroscopeHandler(BaseHTTPRequestHandler):
             else:
                 raise KeyError('Unknown API version: %s' % self.path)
         except KeyError as exc:
-            self.log_error("KeyError raised during handling of GET request '%s': %s" % (self.path, repr(exc)))
+            self.log_error("KeyError raised during handling of GET request '%s': %s" , self.path, repr(exc))
             self.send_error(404, str(exc))
         except Exception as exc:
-            self.log_error("Exception raised during handling of GET request '%s': %s" % (self.path, repr(exc)))
+            self.log_error("Exception raised during handling of GET request '%s': %s" , self.path, repr(exc))
             self.send_error(500, "Error handling request '%s': %s" % (self.path, str(exc)))
         else:
             self.build_response(response)

temscript-2.2.0/temscript/version.py

@@ -0,0 +1 @@
+__version__ = '2.2.0'

{temscript-2.0.1 → temscript-2.2.0/temscript.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: temscript
-Version: 2.0.1
-Summary: TEM Scripting adapter for FEI microscopes
+Version: 2.2.0
+Summary: TEM Scripting adapter for TFS/FEI transmission electron microscopes
 Home-page: https://github.com/niermann/temscript
 Author: Tore Niermann
 Author-email: tore.niermann@tu-berlin.de
@@ -21,6 +21,20 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.4
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: numpy
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # About
 

{temscript-2.0.1 → temscript-2.2.0}/temscript.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ docs/restrictions.rst
 docs/server.rst
 scripts/run_null_server.py
 scripts/test_camera_acquisition.py
+scripts/test_com.py
 scripts/test_instrument.py
 scripts/test_json_encoder.py
 scripts/test_microscope.py

temscript-2.0.1/temscript/version.py

@@ -1 +0,0 @@
-__version__ = '2.0.1'