Added flat acquisition

tomcat_bec/device_configs/microxas_test_bed.yaml

@@ -10,30 +10,20 @@ eyex:
   enabled: true
   readOnly: false
   softwareTrigger: false
-# eyey:
+
-#   readoutPriority: baseline
+eyez:
-#   description: X-ray eye axis Y
+  readoutPriority: baseline
-#   deviceClass: tomcat_bec.devices.psimotor.EpicsMotorEC
+  description: X-ray eye axis Z
-#   deviceConfig:
+  deviceClass: tomcat_bec.devices.psimotor.EpicsMotorEC
-#     prefix: MTEST-X05LA-ES2-XRAYEYE:M2
+  deviceConfig:
-#   deviceTags:
+    prefix: MTEST-X05LA-ES2-XRAYEYE:M3
-#     - xray-eye
+  deviceTags:
-#   onFailure: buffer
+    - xray-eye
-#   enabled: true
+  onFailure: buffer
-#   readOnly: false
+  enabled: true
-#   softwareTrigger: false  
+  readOnly: false
-# eyez:
+  softwareTrigger: false
-#   readoutPriority: baseline
+
-#   description: X-ray eye axis Z
-#   deviceClass: tomcat_bec.devices.psimotor.EpicsMotorEC
-#   deviceConfig:
-#     prefix: MTEST-X05LA-ES2-XRAYEYE:M3
-#   deviceTags:
-#     - xray-eye
-#   onFailure: buffer
-#   enabled: true
-#   readOnly: false
-#   softwareTrigger: false
 femto_mean_curr:
   readoutPriority: monitored
   description: Femto mean current

tomcat_bec/scans/__init__.py

@@ -1,2 +1,2 @@
-from .tutorial_fly_scan import AcquireDark, AcquireFlat, TutorialFlyScanContLine
+from .tutorial_fly_scan import AcquireDark, AcquireWhite, TutorialFlyScanContLine
 from .tomcat_scans import TomcatStepScan, TomcatSnapNStep, TomcatSimpleSequence

tomcat_bec/scans/tutorial_fly_scan.py

@@ -27,7 +27,7 @@ class AcquireDark(Acquire):
         image_height : int, optional
             ROI size in the y-direction [pixels]
         acq_mode : str, optional
-            Predefined acquisition mode (default=)
+            Predefined acquisition mode (default= 'default')
         file_path : str, optional
             File path for standard daq
 
@@ -51,39 +51,58 @@ class AcquireDark(Acquire):
         yield from super().scan_core()
 
 
-class AcquireFlat(Acquire):
+class AcquireWhite(Acquire):
-    scan_name = "acquire_flat"
+    scan_name = "acquire_white"
-    required_kwargs = ["num"]
+    required_kwargs = ["exp_burst", "sample_position_out", "sample_angle_out"]
-    gui_config = {"Acquisition parameters": ["num"]}
+    gui_config = {"Acquisition parameters": ["exp_burst"]}
 
-    def __init__(self, num: int, out_position: float, **kwargs):
+    def __init__(self, exp_burst: int, sample_position_out: float, sample_angle_out: float, **kwargs):
         """
-        Acquire a flat field image. This scan is used to acquire a flat field image. The flat field image is an image taken
+        Acquire flat field images. This scan is used to acquire flat field images. The flat field image is an image taken
-        with the shutter open but the sample out of the beam. The flat field image is used to correct the data images for
+        with the shutter open but the sample out of the beam. Flat field images are used to correct the data images for
         non-uniformity in the detector.
 
         Args:
-            num (int): number of flat field images to acquire
+        exp_burst : int
-            out_position (float): position to move the sample stage to take the flat field image
+            Number of flat field images to acquire (no default)
+        sample_position_out : float
+            Position to move the sample stage to position the sample out of beam and take flat field images
+        sample_angle_out : float
+            Angular position where to take the flat field images
+        exp_time : float, optional
+            Exposure time [ms]. If not specified, the currently configured value on the camera will be used
+        exp_period : float, optional
+            Exposure period [ms]. If not specified, the currently configured value on the camera will be used
+        image_width : int, optional
+            ROI size in the x-direction [pixels]. If not specified, the currently configured value on the camera will be used
+        image_height : int, optional
+            ROI size in the y-direction [pixels]. If not specified, the currently configured value on the camera will be used
+        acq_mode : str, optional
+            Predefined acquisition mode (default= 'default')
+        file_path : str, optional
+            File path for standard daq
 
         Returns:
             ScanReport
 
         Examples:
-            >>> scans.acquire_flat(5, 20)
+            >>> scans.acquire_white(5, 20)
 
         """
         super().__init__(**kwargs)
-        self.burst_at_each_point = num
+        self.burst_at_each_point = 1
-        self.out_position = out_position
+        self.sample_position_out = sample_position_out
-        self.sample_stage = "samy"  # change to the correct sample stage device
+        self.sample_angle_out = sample_angle_out
-        self.shutter = "hx"  # change to the correct shutter device
+
+        self.scan_motors = ["eyex", "eyez", "es1_roty"]  # change to the correct shutter device
+#        self.scan_motors = ["eyex", "eyez"]  # change to the correct shutter device
+        self.dark_shutter_pos = 1 ### change with a variable
+
 
     def scan_core(self):
         # open the shutter and move the sample stage to the out position
-        yield from self.stubs.set_and_wait(
+        yield from self._move_scan_motors_and_wait([self.dark_shutter_pos, self.sample_position_out, self.sample_angle_out])
-            device=[self.shutter, self.sample_stage], positions=[1, self.out_position]
+#        yield from self._move_scan_motors_and_wait([self.dark_shutter_pos, self.sample_position_out])
-        )
         yield from super().scan_core()
 
 
@@ -168,7 +187,7 @@ class TutorialFlyScanContLine(AsyncFlyScanBase):
                 show_asap=True,
                 rid=self.metadata.get("RID"),
             )
-            flats = AcquireFlat(
+            flats = AcquireWhite(
                 num=self.num_flats,
                 exp_time=self.exp_time,
                 out_position=self.sample_out,

tomcat_bec/scripts/scans_fede.py

@@ -12,6 +12,11 @@ class Measurement:
         self.nimages_dark = 50
         self.nimages_white = 100
 
+        self.start_angle = 0
+        self.sample_angle_out = 0
+        self.sample_position_in = 0
+        self.sample_position_out = 1
+
         # To be able to keep what is already set on the camera
         self.exposure_time = None
         self.exposure_period = None
@@ -29,12 +34,20 @@ class Measurement:
         
         self.build_filename()
 
-    def build_filename(self):
+    def build_filename(self, acquisition_type='data'):
         """
         Build and set filepath for bec
         Build filepath and file prefix for stddaq
+
+        acquisition_type : string, optional
+            Type of images: a choice between dark, white, or data (default = data)
         """
         
+        if acquisition_type != "data" and acquisition_type != "dark" and acquisition_type != "white":
+            print("WARNING: chosen acquisition type not permitted! \n")
+            print("The chosen acquitisition type as been set to \"data\"!")
+            acquisition_type == "data"
+
         self.scan_sample_name = 'S' + str(bec.queue.next_scan_number) + '_' + self.sample_name
             
         # File path for bec
@@ -44,11 +57,13 @@ class Measurement:
         self.file_path = os.path.join('/data/test/test-beamline',bec.system_config.file_directory, '_device_dat', self.device_name) # _device_dat does not work for now.        
         # A hack for now to create the right permissions
         self.base_path = os.path.join('/data/test/test-beamline',self.data_path)
-        self.file_prefix = self.scan_sample_name + '_' + self.device_name + '_data_dark_'
+        self.file_prefix = self.scan_sample_name + '_' + self.device_name + '_' + acquisition_type + '_'
 
     def configure(self,sample_name=None, data_path=None, exposure_time=None,
                   exposure_period=None, roix=None, roiy=None,nimages=None,
-                  nimages_dark=None, nimages_white=None):
+                  nimages_dark=None, nimages_white=None,
+                  start_angle=None, sample_angle_out=None,
+                  sample_position_in=None, sample_position_out=None):
         """
         Reconfigure the measurement with any number of new parameter
         
@@ -56,24 +71,34 @@ class Measurement:
         ----------
         sample_name : string, optional
             Name of the sample or measurement. This name will be used to construct
-            the name of the measurement directory (default=None)
+            the name of the measurement directory (default = None)
         data_path : string, optional
             Information used to build the data directory for the measurement 
-            (default=None)
+            (default = None)
         exposure_time : float, optional
-            Exposure time [ms] (default=None)
+            Exposure time [ms] (default = None)
         exposure_period : float, optional
-            Exposure period [ms] (default=None)
+            Exposure period [ms] (default = None)
         roix : int, optional
-            ROI size in the x-direction [pixels] (default=None)
+            ROI size in the x-direction [pixels] (default = None)
         roiy : int, optional
-            ROI size in the y-direction [pixels] (default=None)
+            ROI size in the y-direction [pixels] (default = None)
         nimages : int, optional
-            Number of images to acquire (default=None)
+            Number of images to acquire (default = None)
         nimages_dark : int, optional
-            Number of dark images to acquire (default=None)
+            Number of dark images to acquire (default = None)
         nimages_white : int, optional
-            Number of white images to acquire (default=None)
+            Number of white images to acquire (default = None)
+        start_angle : float, optional
+            The start angle for the scan [deg] (default = None)
+        sample_angle_out : float, optional
+            Sample rotation angle for sample out of the beam [deg]
+             (default = None)
+        sample_position_in : float, optional
+            Sample stage X position for sample in beam [um] (default = None)
+        sample_position_out : float, optional
+            Sample stage X position for sample out of the beam [um]
+            (default = None)
          """
 
         if sample_name != None:
@@ -94,6 +119,14 @@ class Measurement:
             self.roix = roix
         if roiy != None: 
             self.roiy = roiy
+        if start_angle != None:
+            self.start_angle = start_angle
+        if sample_angle_out != None:
+            self.sample_angle_out = sample_angle_out
+        if sample_position_in != None:
+            self.sample_position_in = sample_position_in
+        if sample_position_out != None:
+            self.sample_position_out = sample_position_out
 
         self.build_filename()
 
@@ -102,7 +135,7 @@ class Measurement:
         """
         Show configuration
 
-        TODO: check active devices, write the config for each device and if none read from device
+        TODO: make it work for multiple devices
         """
 
         print("Sample name: " + self.sample_name)
@@ -110,11 +143,28 @@ class Measurement:
         print("Number of images: " + str(self.nimages))
         print("Number of darks: " + str(self.nimages_dark))
         print("Number of flats: " + str(self.nimages_white))
-        print("Exposure time: " + str(self.exposure_time))
+        if self.exposure_time == None:
-        print("Exposure period: " + str(self.exposure_period))
+            print("Exposure time: " + str(self.det.cfgExposure.get()))
-        print("Roix: " + str(self.roix))
+        else:
-        print("Roiy: " + str(self.roiy))
+            print("Exposure time: " + str(self.exposure_time))
+        if self.exposure_period == None:
+            print("Exposure peirod: " + str(self.det.cfgFramerate.get()))
+        else:   
+            print("Exposure period: " + str(self.exposure_period))
+        if self.roix == None:
+            print("Roix: " + str(self.det.cfgRoiX.get()))
+        else:
+            print("Roix: " + str(self.roix))
+        if self.roiy == None:
+            print("Roiy: " + str(self.det.cfgRoiY.get()))
+        else:
+            print("Roiy: " + str(self.roiy))
+        print("Start angle: " + str(self.start_angle))
+        print("Sample angle out: " + str(self.sample_angle_out))
+        print("Sample position in: " + str(self.sample_position_in))
+        print("Sample position out: " + str(self.sample_position_out))
         
+    
     def acquire_darks(self,nimages_dark, exposure_time=None, exposure_period=None, 
                       roix=None, roiy=None, acq_mode=None):
         """
@@ -137,7 +187,7 @@ class Measurement:
 
         Example:
         --------
-        fede_darks(100, exposure_time=5)
+        m.acquire_darks(100, exposure_time=5)
         """
         # dev.es1_tasks.enabled = False
         # dev.es1_psod.enabled = False
@@ -158,10 +208,71 @@ class Measurement:
         if roiy != None:
             self.roiy = roiy
         
-        self.build_filename()
+        self.build_filename(acquisition_type='dark')
 
         ### TODO: camera reset
         print("Handing over to 'scans.acquire_dark")
         scans.acquire_dark(exp_burst=nimages_dark, exp_time=self.exposure_time, exp_period=self.exposure_period, image_width=self.roix, 
                            image_height=self.roiy, acq_mode=acq_mode, file_path=self.file_path, nr_writers=2, base_path=self.base_path,
-                           file_prefix=self.file_prefix)
+                           file_prefix=self.file_prefix)
+        
+    def acquire_whites(self,nimages_whites, sample_angle_out=None, sample_position_out=None,
+                       exposure_time=None, exposure_period=None,
+                       roix=None, roiy=None, acq_mode=None):
+        """
+        Acquire a set of whites images with shutters open and sample out of beam.
+
+        Parameters
+        ----------
+        nimages_whites : int
+            Number of white images to acquire (no default)
+        sample_angle_out : float, optional
+            Sample rotation angle for sample out of the beam [deg]
+        sample_position_out : float, optional
+            Sample stage X position for sample out of the beam [um]
+        exposure_time : float, optional
+            Exposure time [ms]. If not specified, the currently configured value on the camera will be used
+        exposure_period : float, optional
+            Exposure period [ms]
+        roix : int, optional
+            ROI size in the x-direction [pixels]
+        roiy : int, optional
+            ROI size in the y-direction [pixels]
+        acq_mode : str, optional
+            Predefined acquisition mode (default=None)
+
+        Example:
+        --------
+        m.acquire_whites(100, exposure_time=5)
+        """
+        # dev.es1_tasks.enabled = False
+        # dev.es1_psod.enabled = False
+        # dev.es1_ddaq.enabled = False
+        # dev.es1_ismc.enabled = False
+        # dev.es1_roty.enabled = False
+        dev.gfcam.enabled = True
+        dev.gfdaq.enabled = True
+        dev.daq_stream0.enabled = True
+        dev.daq_stream1.enabled = False
+
+        if sample_angle_out != None:
+            self.sample_angle_out = sample_angle_out
+        if sample_position_out != None:
+            self.sample_position_out = sample_position_out
+        if exposure_time != None:
+            self.exposure_time = exposure_time
+        if exposure_period != None:
+            self.exposure_period = exposure_period
+        if roix != None:
+            self.roix = roix
+        if roiy != None:
+            self.roiy = roiy
+        
+        self.build_filename(acquisition_type='white')
+
+        ### TODO: camera reset
+        print("Handing over to 'scans.acquire_whites")
+        scans.acquire_white(exp_burst=nimages_whites, sample_angle_out=self.sample_angle_out, sample_position_out= self.sample_position_out,
+                             exp_time=self.exposure_time, exp_period=self.exposure_period, image_width=self.roix,
+                             image_height=self.roiy, acq_mode=acq_mode, file_path=self.file_path, nr_writers=2, base_path=self.base_path,
+                             file_prefix=self.file_prefix)