Squashed commit of the following:

commit c2b3dc5
Author: Ian Dobbie <[email protected]>
Date:   Tue Aug 22 12:21:54 2023 -0400

    Added the required getValues function to the raspberrypi valueLogger module.

commit fa592d6
Author: David Miguel Susano Pinto <[email protected]>
Date:   Tue Aug 22 13:52:42 2023 +0100

    RPiValueLogger: check for availability of MCP9808 and TSYS01 classes.

commit bcd3d86
Author: David Miguel Susano Pinto <[email protected]>
Date:   Tue Aug 22 13:44:11 2023 +0100

    PiCamera: use ROI field names instead of tuple index for readability

commit 8f631d7
Author: David Miguel Susano Pinto <[email protected]>
Date:   Tue Aug 22 13:42:07 2023 +0100

    maint: black and isort for consistent style.

commit 03e6b5c
Author: David Miguel Susano Pinto <[email protected]>
Date:   Tue Aug 22 12:42:09 2023 +0100

    Use a standard search path for DLL loading in windows (python-microscope#235)

    Since Python 3.8, ctypes uses an altered search path when loading DLLs
    in Windows which only includes the application directory, the system32
    directory, and directories manually specified with add_dll_directory.
    None of those suit us.  The standard search path can be specified with
    `winmode=0`.

    This commit adds a new function to loads libraries with `winmode=0`
    and makes all modules that load shared libraries use it.

commit 6a4ee44
Author: Ian Dobbie <[email protected]>
Date:   Mon Aug 21 14:01:48 2023 -0400

    Fix picamera roi code to use the ROI named tuples and then just return roi python-microscope#279

commit 76a6364
Author: Ian Dobbie <[email protected]>
Date:   Mon Jul 24 22:09:11 2023 -0400

    Added pulldata option to allow cockpit to pull data from valuelogger devices

NEWS.rst

@@ -67,6 +67,11 @@ Version 0.7.0 (upcoming)
 
 * Microscope is now dependent on Python 3.7 or later.
 
+* Python 3.8 changed the default DLL search path in Windows which
+  caused all cameras, deformable mirrors, and Linkam stage to fail to
+  load.  This version restores the use of Windows standard search
+  path.
+
 
 Version 0.6.0 (2021/01/14)
 --------------------------

microscope/_utils.py

@@ -17,30 +17,17 @@
 ## You should have received a copy of the GNU General Public License
 ## along with Microscope.  If not, see <http://www.gnu.org/licenses/>.
 
-import threading
-import typing
+import ctypes
 import os
 import sys
-import ctypes
+import threading
+import typing
 
 import serial
 
 import microscope
 import microscope.abc
 
-def load_library(windows_file=None, unix_file=None):
-    kwargs = {}
-    if windows_file is not None and os.name == "nt":
-        dll = windows_file
-        if sys.version_info >= (3, 8):
-            kwargs["winmode"] = 0
-    elif unix_file is not None:
-        dll = unix_file
-    else:
-        raise OSError("Unable to laod DLL")
-
-    return ctypes.CDLL(dll, **kwargs)
-
 
 # Both pySerial and serial distribution packages install an import
 # package named serial.  If both are installed we may have imported
@@ -59,6 +46,36 @@ def load_library(windows_file=None, unix_file=None):
         )
 
 
+def library_loader(
+    libname: str, dlltype: typing.Type[ctypes.CDLL] = ctypes.CDLL, **kwargs
+) -> ctypes.CDLL:
+    """Load shared library.
+
+    This exists mainly to search for DLL in Windows using a standard
+    search path, i.e, search for dlls in ``PATH``.
+
+    Args:
+        libname: file name or path of the library to be loaded as
+            required by `dlltype`
+        dlltype: the class of shared library to load.  Typically,
+            ``CDLL`` but sometimes ``WinDLL`` in windows.
+        kwargs: other arguments passed on to ``dlltype``.
+    """
+    # Python 3.8 in Windows uses an altered search path.  Their
+    # reasons is security and I guess it would make sense if we
+    # installed the DLLs we need ourselves but we don't.  `winmode=0`
+    # restores the use of the standard search path.  See issue #235.
+    if (
+        os.name == "nt"
+        and sys.version_info >= (3.8)
+        and "winmode" not in kwargs
+    ):
+        winmode_kwargs = {"winmode": 0}
+    else:
+        winmode_kwargs = {}
+    return dlltype(libname, **winmode_kwargs, **kwargs)
+
+
 class OnlyTriggersOnceOnSoftwareMixin(microscope.abc.TriggerTargetMixin):
     """Utility mixin for devices that only trigger "once" with software.
 

microscope/_wrappers/BMC.py

@@ -21,11 +21,18 @@
 """
 
 import ctypes
+import os
 from ctypes import c_char, c_char_p, c_double, c_int, c_uint, c_uint32
-from microscope._utils import load_library
 
-# Not actually tested BMC2 yet
-SDK = load_library(windows_file="BMC2", unix_file="libBMC.so.3")
+import microscope._utils
+
+
+if os.name == "nt":  # is windows
+    # Not actually tested yet
+    SDK = microscope._utils.library_loader("BMC2", ctypes.WinDLL)
+else:
+    SDK = microscope._utils.library_loader("libBMC.so.3")
+
 
 # Definitions from BMCDefs.h
 MAX_PATH = 260

microscope/_wrappers/asdk.py

@@ -21,10 +21,18 @@
 """
 
 import ctypes
+import os
 from ctypes import c_char_p, c_double, c_int, c_size_t, c_uint32
-from microscope._utils import load_library
 
-SDK = load_library(windows_file="ASDK", unix_file="libasdk.so")
+import microscope._utils
+
+
+if os.name == "nt":  # is windows
+    _libname = "ASDK"
+else:
+    _libname = "libasdk.so"  # Not actually tested yet
+SDK = microscope._utils.library_loader(_libname)
+
 
 class DM(ctypes.Structure):
     pass

microscope/_wrappers/dcamapi4.py

@@ -34,11 +34,13 @@
 import enum
 import os
 
+import microscope._utils
+
 
 if os.name == "nt":
-    _LIB = ctypes.WinDLL("dcamapi")
+    _LIB = microscope._utils.library_loader("dcamapi", ctypes.WinDLL)
 else:
-    _LIB = ctypes.CDLL("libdcamapi.so")
+    _LIB = microscope._utils.library_loader("libdcamapi.so", ctypes.CDLL)
 
 
 if os.name == "nt":

microscope/_wrappers/mirao52e.py

@@ -22,10 +22,12 @@
 
 import ctypes
 
-from microscope._utils import load_library
+import microscope._utils
+
 
 # Vendor only supports Windows
-SDK = load_library(windows_file="mirao52e")
+SDK = microscope._utils.library_loader("mirao52e", ctypes.WinDLL)
+
 
 TRUE = 1  # TRUE MroBoolean value
 FALSE = 0  # FALSE MroBoolean value

microscope/abc.py

@@ -1696,13 +1696,17 @@ class ValueLogger(DataDevice, metaclass=abc.ABCMeta):
         numSensors: total number of measurements.
 
     """
-    def __init__(self, numSensors: int, **kwargs) -> None:
+
+    def __init__(self, numSensors: int, pullData: bool, **kwargs) -> None:
         super().__init__(**kwargs)
         if numSensors < 1:
             raise ValueError(
                 "NumSensors must be a positive number (was %d)" % numSensors
             )
         self._numSensors = numSensors
+        # If pull data is True data will be pulled from the server if False
+        # data will be pushed from microsocpe (default)
+        self.pullData = pullData
 
     @abc.abstractmethod
     def initialize(self):
@@ -1712,3 +1716,8 @@ def initialize(self):
     def get_num_sensors(self):
         """Returns the number of sensors lines present in this instance."""
         return self._numSensors
+
+    @abc.abstractmethod
+    def getValues(self):
+        """Returns values from all sensors"""
+        raise NotImplementedError()

microscope/cameras/_SDK3.py

@@ -20,9 +20,11 @@
 ## along with Microscope.  If not, see <http://www.gnu.org/licenses/>.
 
 import ctypes
+import os
 from ctypes import POINTER, c_double, c_int, c_uint, c_void_p
 
-from microscope._utils import load_library
+import microscope._utils
+
 
 #### typedefs
 AT_H = ctypes.c_int
@@ -31,12 +33,24 @@
 AT_U8 = ctypes.c_uint8
 AT_WC = ctypes.c_wchar
 
-_stdcall_libraries = {
-    "ATCORE": load_library(windows_file="atcore", unix_file="atcore.so"),
-    "ATUTIL": load_library(windows_file="atutility", unix_file="atutility.so")
-}
-
-CALLBACKTYPE = ctypes.WINFUNCTYPE(c_int, AT_H, POINTER(AT_WC), c_void_p)
+_stdcall_libraries = {}
+
+if os.name == "nt":  # is windows
+    _stdcall_libraries["ATCORE"] = microscope._utils.library_loader(
+        "atcore", ctypes.WinDLL
+    )
+    _stdcall_libraries["ATUTIL"] = microscope._utils.library_loader(
+        "atutility", ctypes.WinDLL
+    )
+    CALLBACKTYPE = ctypes.WINFUNCTYPE(c_int, AT_H, POINTER(AT_WC), c_void_p)
+else:
+    _stdcall_libraries["ATCORE"] = microscope._utils.library_loader(
+        "atcore.so"
+    )
+    _stdcall_libraries["ATUTIL"] = microscope._utils.library_loader(
+        "atutility.so"
+    )
+    CALLBACKTYPE = ctypes.CFUNCTYPE(c_int, AT_H, POINTER(AT_WC), c_void_p)
 
 #### Defines
 errorCodes = {}

microscope/cameras/atmcd.py

@@ -64,8 +64,8 @@
 from numpy.ctypeslib import ndpointer
 
 import microscope
+import microscope._utils
 import microscope.abc
-from microscope._utils import load_library
 
 
 _logger = logging.getLogger(__name__)
@@ -88,7 +88,10 @@
     _dllName = "atmcd32d"
 else:
     _dllName = "atmcd64d"
-_dll = load_library(windows_file=_dllName, unix_file=_dllName + ".so")
+if os.name == "nt":  # is windows
+    _dll = microscope._utils.library_loader(_dllName, ctypes.WinDLL)
+else:
+    _dll = microscope._utils.library_loader(_dllName + ".so")
 
 # Andor's types
 at_32 = c_long

microscope/cameras/picamera.py

@@ -226,9 +226,9 @@ def _get_binning(self):
         return Binning(1, 1)
 
     @keep_acquiring
-    def _set_roi(self, left, top, width, height):
-        """Set the ROI to (left, tip, width, height)."""
-        self.roi = ROI(left, top, width, height)
+    def _set_roi(self, region):
+        """Set the ROI to the name tuple ROI(left, top, width, height)."""
+        self.roi = region
 
     # set camera LED status, off is best for microscopy.
     def setLED(self, state=False):
@@ -252,7 +252,7 @@ def _get_sensor_shape(self):
             self.camera.resolution = (2592, 1944)
         # faqll back to defualt if not set above.
         res = self.camera.resolution
-        self._set_roi(0, 0, res[0], res[1])
+        self._set_roi(ROI(0, 0, res[0], res[1]))
         return res
 
     def _do_trigger(self):
@@ -265,7 +265,13 @@ def soft_trigger(self):
         if self._acquiring:
             with picamera.array.PiYUVArray(self.camera) as output:
                 self.camera.capture(output, format="yuv", use_video_port=False)
-                self._queue.put(output.array[:, :, 0])
+                self._queue.put(
+                    output.array[
+                        self.roi.top : self.roi.top + self.roi.height,
+                        self.roi.left : self.roi.left + self.roi.width,
+                        0,
+                    ]
+                )
 
 
 # ongoing implemetation notes

microscope/cameras/pvcam.py

@@ -136,7 +136,6 @@
 import ctypes
 import logging
 import os
-import sys
 import platform
 import time
 import weakref
@@ -145,8 +144,8 @@
 import Pyro4
 
 import microscope
+import microscope._utils
 import microscope.abc
-from microscope._utils import load_library
 
 
 _logger = logging.getLogger(__name__)
@@ -675,11 +674,14 @@ class md_frame(ctypes.Structure):
         ("roiCount", uns16),
     ]
 
-def _load_lib():
-    _dllsuffix = platform.architecture()[0].rstrip("bit")
-    return load_library(windows_file="pvcam" + _dllsuffix, unix_file="pvcam.so")
 
-_lib = _load_lib()
+if os.name == "nt":  # is windows
+    if platform.architecture()[0] == "32bit":
+        _lib = microscope._utils.library_loader("pvcam32", ctypes.WinDLL)
+    else:
+        _lib = microscope._utils.library_loader("pvcam64", ctypes.WinDLL)
+else:
+    _lib = microscope._utils.library_loader("pvcam.so")
 
 
 ### Functions ###

microscope/controllers/ludl.py

@@ -203,10 +203,10 @@ def move_command(self, command: bytes) -> None:
         self._command_and_validate(command, b"N")
         #
         # No Following is not true as Cockpit expects moves to happen
-        # before the return. 
+        # before the return.
         # actully beter to just issue the move command and rely on
         # other process to check position
-        #self.get_command(command)
+        # self.get_command(command)
 
     def move_by_relative_position(self, axis: bytes, delta: float) -> None:
         """Send a relative movement command to stated axis"""

microscope/digitalio/raspberrypi.py

@@ -23,16 +23,17 @@
 """
 
 import contextlib
+import logging
+import queue
 import re
 import threading
 import time
 import typing
-import logging
-import queue
-import microscope.abc
 
 import RPi.GPIO as GPIO
 
+import microscope.abc
+
 
 # Support for async digital IO control on the Raspberryy Pi.
 # Currently supports digital input and output via GPIO lines