AndorCamera: * Correctly reshape arrays returned by GetAcquiredData and GetOldestImage16

* Add uninitialised emccd_gain instance attribute for debug messages
* Do not modify defauld acquisition attributes dict, ensure a copy is used
* Only print debug info about temperature if cooling is enabled
* Missing attribute rename trig_capability -> trig_caps
* Move SetImage call to outside an if statement, since it occurs unconditionally
* Fix two syntax errors
* Simplified reshaping in download_acquisition.
* Switch to GetAcquiredData instead of GetOldestImage16 in non-fast-kinetics
* Return a 3D array from snap() so that fast kinetics results are displayable
  in the BLACS tab.
* Modify IMAQdxCamera tab to display a 3D array of images with only one image
  as a 2D array

Author: rb_chip

AndorSolis/andor_sdk/andor_solis.py

@@ -305,7 +305,7 @@ def GetAcquiredData(shape):
     arr = (ctypes.c_int32 * size)()
     result = andor_solis.GetAcquiredData(ctypes.pointer(arr), ctypes.c_ulong(size))
     check_status(result)
-    return np.ctypeslib.as_array(arr)
+    return np.ctypeslib.as_array(arr).reshape(shape)
 
 def GetAcquiredData16(shape):
     """ 16-bit version of the GetAcquiredData function. 
@@ -316,7 +316,7 @@ def GetAcquiredData16(shape):
     arr = (ctypes.c_uint16 * size)()  # not 100% sure this should be unsigned.
     result = andor_solis.GetAcquiredData16(ctypes.pointer(arr), ctypes.c_ulong(size))
     check_status(result)
-    return np.ctypeslib.as_array(arr)
+    return np.ctypeslib.as_array(arr).reshape(shape)
 
 def GetAcquiredFloatData(shape):
     """ This function is reserved """

AndorSolis/andor_sdk/andor_utils.py

@@ -61,6 +61,7 @@ def __init__(self, name='andornymous'):
         self.cooling = False
         self.preamp = False
         self.emccd = False
+        self.emccd_gain = None
         self.armed = False
         self.initialize_camera()
 
@@ -240,7 +241,7 @@ def setup_vertical_shift(self, custom_option=1):
             self.index_vs_speed = custom_option
 
             # For FastKinetics mode the calls are different
-            if 'fast_kinetics' in self.acquisition_mode
+            if 'fast_kinetics' in self.acquisition_mode:
                 number_fkvs_speeds = GetNumberFKVShiftSpeeds()
                 if not custom_option in range(number_fkvs_speeds):
                     raise ValueError("Invalid vertical shift speed custom option value")
@@ -281,15 +282,16 @@ def setup_horizontal_shift(self, custom_option=None):
         # Get actual horizontal shifting (i.e. digitization) speed
         self.horizontal_shift_speed = GetHSSpeed(ad_number, 0, self.index_hs_speed)
 
-    def setup_acquisition(self, added_attributes={}):
+    def setup_acquisition(self, added_attributes=None):
         """ Main acquisition configuration method. Available acquisition modes are
         below. The relevant methods are called with the corresponding acquisition 
         attributes dictionary, then the camera is armed and ready """
+        if added_attributes is None:
+            added_attributes = {}
 
         # Override default acquisition attrs with added ones
-        self.acquisition_attributes = self.default_acquisition_attrs
-        for attr, val in added_attributes.items():
-            self.acquisition_attributes[attr] = val
+        self.acquisition_attributes = self.default_acquisition_attrs.copy()
+        self.acquisition_attributes.update(added_attributes)
 
         self.acquisition_mode = self.acquisition_attributes['acquisition']
 
@@ -305,14 +307,14 @@ def setup_acquisition(self, added_attributes={}):
                 self.acquisition_attributes['water_cooling'],
             )
 
-        # Get current temperature and temperature status
-        self.temperature, self.temperature_status = GetTemperatureF()
-        if self.chatty:
-            rich_print(
-                f"""At setup_acquisition the temperature is: 
-                {self.temperature}; with status {self.temperature_status}""",
-                color='magenta',
-            )
+            # Get current temperature and temperature status
+            self.temperature, self.temperature_status = GetTemperatureF()
+            if self.chatty:
+                rich_print(
+                    f"""At setup_acquisition the temperature is: 
+                    {self.temperature}; with status {self.temperature_status}""",
+                    color='magenta',
+                )
 
         # Available modes
         modes = {
@@ -447,7 +449,7 @@ def setup_trigger(self, **attrs):
         SetTriggerMode(modes[attrs['trigger']])
 
         # Specify edge if invertible trigger capability is present
-        if 'INVERT' in self.trig_capability:
+        if 'INVERT' in self.trig_caps:
             SetTriggerInvert(edge_modes[attrs['trigger_edge']])
 
         if attrs['trigger'] == 'external':
@@ -499,9 +501,8 @@ def setup_readout(self, **attrs):
             attrs['width'] = 1
 
         self.image_shape = (
-            int(attrs['number_kinetics']),
-            int(attrs['height']/attrs['ybin']),
-            int(attrs['width']/attrs['xbin']),
+            attrs['height'] // attrs['ybin'],
+            attrs['width'] // attrs['xbin'],
         )
 
         # For a full-frame kinetic series, we simply set the frame for readout. 
@@ -511,26 +512,18 @@ def setup_readout(self, **attrs):
         # self.emgain_caps). For higher ranges use SetEMGainMode(). We also need to
         # enable the frame transfer mode.
         if self.acquisition_mode == 'kinetic_series':
-            SetImage(
-                attrs['xbin'],
-                attrs['ybin'],
-                attrs['left_start'],
-                attrs['width'] + attrs['left_start'] - 1,
-                attrs['bottom_start'],
-                attrs['height'] + attrs['bottom_start'] - 1,
-            )
             if self.acquisition_attributes['crop']:
-            SetOutputAmplifier(0)
-            SetFrameTransferMode(1)
-            SetIsolatedCropModeEx(
-                int(1),
-                int(attrs['height']),
-                int(attrs['width']),
-                attrs['ybin'],
-                attrs['xbin'],
-                attrs['left_start'],
-                attrs['bottom_start'],
-            )
+                SetOutputAmplifier(0)
+                SetFrameTransferMode(1)
+                SetIsolatedCropModeEx(
+                    int(1),
+                    int(attrs['height']),
+                    int(attrs['width']),
+                    attrs['ybin'],
+                    attrs['xbin'],
+                    attrs['left_start'],
+                    attrs['bottom_start'],
+                )
         else:
             SetFrameTransferMode(0)
             SetIsolatedCropModeEx(
@@ -542,14 +535,14 @@ def setup_readout(self, **attrs):
                 attrs['left_start'],
                 attrs['bottom_start'],
             )
-            SetImage(
-                attrs['xbin'],
-                attrs['ybin'],
-                attrs['left_start'],
-                attrs['width'] + attrs['left_start'] - 1,
-                attrs['bottom_start'],
-                attrs['height'] + attrs['bottom_start'] - 1,
-            )
+        SetImage(
+            attrs['xbin'],
+            attrs['ybin'],
+            attrs['left_start'],
+            attrs['width'] + attrs['left_start'] - 1,
+            attrs['bottom_start'],
+            attrs['height'] + attrs['bottom_start'] - 1,
+        )
 
     def acquire(self):
         """ Carries down the acquisition, if the camera is armed and
@@ -606,15 +599,16 @@ def homemade_wait_for_acquisition():
                 AbortAcquisition()
                 raise AndorException('Acquisition aborted due to timeout')
 
-    def download_acquisition(self,):
-        """ Download buffered acquisition """
-        shape = self.image_shape
-
-        # Various useful FK image shapes
+    def download_acquisition(self):
+        """ Download buffered acquisition. For fast kinetics, returns a 3D
+        array of shape (N_fast_kinetics, Ny//N, Nx). Otherwise, returns array
+        of shape (N_exposures, Ny, Nx)."""
+        
+        N = self.acquisition_attributes['number_kinetics']
         if 'fast_kinetics' in self.acquisition_mode:
-            fk_read_shape = (1, *shape[1::])
-            fk_single_shape = (shape[1] // shape [0], shape[2])
-            fk_save_shape = (shape[0], shape[1] // shape[0], shape[2])
+            shape = (N, self.image_shape[0] // N, self.image_shape[1])
+        else:
+            shape = (N, self.image_shape[0], self.image_shape[1])
 
         # self.abort_acquisition # This seems like a bad thing to do here...
 
@@ -625,23 +619,24 @@ def download_acquisition(self,):
                 f"Number of available images in the circular buffer is {available_images}."
             )
 
-        if (available_images[1] - available_images[0]) + 1 == shape[0]:
+        if (available_images[1] - available_images[0]) + 1 == N:
             # Special save format for FK frames
             if 'fast_kinetics' in self.acquisition_mode:
-                fk_data = GetAcquiredData(fk_read_shape)
-                data = np.array(fk_data).reshape(fk_save_shape)
+                data = GetAcquiredData(shape)
                 if self.chatty:
                     print(
-                        f"Shape of the downloaded images in FK mode are {fk_save_shape}"
+                        f"Shape of the downloaded images in FK mode are {data.shape}"
                     )
             # Regular save format for other acquisition modes
             else:
-                # data = GetAcquiredData(shape)
-                data = GetOldestImage16(*shape[1::])
+                print("Shape passed to GetAcquiredData is", shape)
+                data = GetAcquiredData(shape)
+                # data = GetOldestImage16(shape)
+                print("Data shape and dtype is:", data.shape, data.dtype)
         else:
             print(
                 f"""------> Incorrect number of images to download: 
-                {available_images}, expecting: {shape[0]}."""
+                {available_images}, expecting: {N}."""
             )
             data = np.zeros(shape)
 

AndorSolis/blacs_workers.py

@@ -39,7 +39,7 @@ def snap(self):
         self.camera.acquire()
         images = self.camera.download_acquisition()
         print(f'Exposure time was {self.camera.exposure_time}')
-        return images[-1] # return last element
+        return images # This may be a 3D array of several images
 
     def configure_acquisition(self, continuous=False, bufferCount=None):
         self.camera.setup_acquisition(self.attributes)
@@ -68,7 +68,7 @@ def grab_multiple(self, n_images, images, waitForNextBuffer=True):
             print(f"FK mode Kinetics Number is {self.camera.number_fast_kinetics}.")
         print(f"    ---> Attempting to grab {n_images} acquisition(s).")
 
-        if 'single' in self.camera.acquisition_mode:            
+        if 'single' in self.camera.acquisition_mode:
             for image_number in range(n_images):
                 self.camera.acquire()
                 print(f"    {image_number}: Acquire complete")
@@ -79,7 +79,7 @@ def grab_multiple(self, n_images, images, waitForNextBuffer=True):
             self.camera.armed = False
             print(f"Got {len(images)} of {n_images} acquisition(s).")
         elif 'fast_kinetics' in self.camera.acquisition_mode:
-            nacquisitions = n_images // self.camera.number_fast_kinetics              
+            nacquisitions = n_images // self.camera.number_fast_kinetics
             for image_number in range(nacquisitions):
                 self.camera.acquire()
                 print(f"    {image_number}: Acquire complete")

IMAQdxCamera/blacs_tabs.py

@@ -68,6 +68,9 @@ def handler(self, data):
         md = json.loads(data[0])
         image = np.frombuffer(memoryview(data[1]), dtype=md['dtype'])
         image = image.reshape(md['shape'])
+        if len(image.shape) == 3 and image.shape[0] == 1:
+            # If only one image given as a 3D array, convert to 2D array:
+            image = image.reshape(image.shape[1:])
         this_frame_time = perf_counter()
         if self.last_frame_time is not None:
             dt = this_frame_time - self.last_frame_time