def stop_scan(global_PVs, params):
log.info(' ')
log.error(' *** Stopping the scan: PLEASE WAIT')
global_PVs['Motor_SampleRot_Stop'].put(1)
global_PVs['HDF1_Capture'].put(0)
aps2bm.wait_pv(global_PVs['HDF1_Capture'], 0)
flir.init(global_PVs, params)
log.error(' *** Stopping scan: Done!')
def acquire(global_PVs, params):
theta = []
# Estimate the time needed for the flyscan
angular_range = params.sample_rotation_end - params.sample_rotation_start
flyscan_time_estimate = angular_range / params.slew_speed
# log.info(' ')
log.warning(' *** Fly Scan Time Estimate: %4.2f minutes' %
(flyscan_time_estimate / 60.))
global_PVs['Cam1_FrameType'].put(FrameTypeData, wait=True)
time.sleep(2)
# global_PVs['Cam1_AcquireTime'].put(float(params.exposure_time) )
if (params.recursive_filter == False):
params.recursive_filter_n_images = 1
num_images = int(params.num_projections) * params.recursive_filter_n_images
global_PVs['Cam1_NumImages'].put(num_images, wait=True)
# Set detectors
if (params.camera_ioc_prefix == '2bmbPG3:'):
global_PVs['Cam1_TriggerMode'].put('Overlapped', wait=True)
elif (params.camera_ioc_prefix == '2bmbSP1:'):
global_PVs['Cam1_TriggerMode'].put('On', wait=True)
# start acquiring
global_PVs['Cam1_Acquire'].put(DetectorAcquire)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], 1)
log.info(' ')
log.info(' *** Fly Scan: Start!')
global_PVs['Fly_Run'].put(1, wait=True)
# wait for acquire to finish
aps2bm.wait_pv(global_PVs['Fly_Run'], 0)
# if the fly scan wait times out we should call done on the detector
# if aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle, flyscan_time_estimate) == False:
if aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle, 5) == False:
global_PVs['Cam1_Acquire'].put(DetectorIdle)
# got error here once when missing 100s of frames: aps2bm.wait_pv( 2bmbSP1:cam1:Acquire 0 5 ) reached max timeout. Return False
log.info(' *** Fly Scan: Done!')
# Set trigger mode to internal for post dark and white
if (params.camera_ioc_prefix == '2bmbPG3:'):
global_PVs['Cam1_TriggerMode'].put('Internal')
elif (params.camera_ioc_prefix == '2bmbSP1:'):
global_PVs['Cam1_TriggerMode'].put('Off', wait=True)
theta = global_PVs['Theta_Array'].get(count=int(params.num_projections))
if (params.recursive_filter_n_images > 1):
theta = np.mean(theta.reshape(-1, params.recursive_filter_n_images),
axis=1)
return theta
def _setup_hdf_writer(global_PVs, params, fname=None):
if (params.camera_ioc_prefix == '2bmbPG3:') or (params.camera_ioc_prefix
== '2bmbSP1:'):
# setup Point Grey hdf writer PV's
log.info(' ')
log.info(' *** setup hdf_writer')
_setup_frame_type(global_PVs, params)
if params.recursive_filter == True:
log.info(' *** Recursive Filter Enabled')
global_PVs['Proc1_Enable_Background'].put('Disable', wait=True)
global_PVs['Proc1_Enable_FlatField'].put('Disable', wait=True)
global_PVs['Proc1_Enable_Offset_Scale'].put('Disable', wait=True)
global_PVs['Proc1_Enable_Low_Clip'].put('Disable', wait=True)
global_PVs['Proc1_Enable_High_Clip'].put('Disable', wait=True)
global_PVs['Proc1_Callbacks'].put('Enable', wait=True)
global_PVs['Proc1_Filter_Enable'].put('Enable', wait=True)
global_PVs['HDF1_ArrayPort'].put('PROC1', wait=True)
global_PVs['Proc1_Filter_Type'].put(Recursive_Filter_Type,
wait=True)
global_PVs['Proc1_Num_Filter'].put(int(
params.recursive_filter_n_images),
wait=True)
global_PVs['Proc1_Reset_Filter'].put(1, wait=True)
global_PVs['Proc1_AutoReset_Filter'].put('Yes', wait=True)
global_PVs['Proc1_Filter_Callbacks'].put('Array N only', wait=True)
log.info(' *** Recursive Filter Enabled: Done!')
else:
global_PVs['Proc1_Filter_Enable'].put('Disable')
global_PVs['HDF1_ArrayPort'].put(
global_PVs['Proc1_ArrayPort'].get())
global_PVs['HDF1_AutoSave'].put('Yes')
global_PVs['HDF1_DeleteDriverFile'].put('No')
global_PVs['HDF1_EnableCallbacks'].put('Enable')
global_PVs['HDF1_BlockingCallbacks'].put('No')
# if (params.recursive_filter == False):
# params.recursive_filter_n_images = 1
totalProj = ((int(params.num_projections / params.recursive_filter_n_images)) + int(params.num_dark_images) + \
int(params.num_white_images))
global_PVs['HDF1_NumCapture'].put(totalProj)
global_PVs['HDF1_FileWriteMode'].put(str(params.file_write_mode),
wait=True)
if fname is not None:
global_PVs['HDF1_FileName'].put(str(fname), wait=True)
global_PVs['HDF1_Capture'].put(1)
aps2bm.wait_pv(global_PVs['HDF1_Capture'], 1)
log.info(' *** setup hdf_writer: Done!')
else:
log.error('Detector %s is not defined' % params.camera_ioc_prefix)
return
def take_image(global_PVs, params):
log.info(' *** *** taking a single image')
nRow = global_PVs['Cam1_SizeY_RBV'].get()
nCol = global_PVs['Cam1_SizeX_RBV'].get()
image_size = nRow * nCol
global_PVs['Cam1_NumImages'].put(1, wait=True)
global_PVs['Cam1_TriggerMode'].put('Off', wait=True)
wait_time_sec = int(params.exposure_time) + 5
global_PVs['Cam1_Acquire'].put(DetectorAcquire, wait=True, timeout=1000.0)
time.sleep(0.1)
if aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle,
wait_time_sec) == False: # adjust wait time
global_PVs['Cam1_Acquire'].put(DetectorIdle)
# Get the image loaded in memory
img_vect = global_PVs['Cam1_Image'].get(count=image_size)
img = np.reshape(img_vect, [nRow, nCol])
pixelFormat = global_PVs['Cam1PixelFormat_RBV'].get(as_string=True)
if (pixelFormat == "Mono16"):
pixel_f = 16
elif (pixelFormat == "Mono8"):
pixel_f = 8
else:
log.error(' *** *** bit %s format not supported' % pixelFormat)
exit()
img_uint = np.mod(img, 2**pixel_f)
return img_uint
def acquire_flat(global_PVs, params):
log.info(' *** White Fields')
global_PVs['Cam1_ImageMode'].put('Multiple')
global_PVs['Cam1_FrameType'].put(FrameTypeWhite)
if (params.camera_ioc_prefix == '2bmbPG3:'):
global_PVs['Cam1_TriggerMode'].put('Overlapped')
elif (params.camera_ioc_prefix == '2bmbSP1:'):
global_PVs['Cam1_TriggerMode'].put('Off', wait=True)
# Set detectors
if (params.camera_ioc_prefix == '2bmbPG3:'):
wait_time_sec = int(params.exposure_time) + 5
global_PVs['Cam1_NumImages'].put(1)
for i in range(
int(params.num_white_images) *
params.recursive_filter_n_images):
global_PVs['Cam1_Acquire'].put(DetectorAcquire)
time.sleep(0.1)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorAcquire, 2)
time.sleep(0.1)
global_PVs['Cam1_SoftwareTrigger'].put(1, wait=True)
time.sleep(0.1)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle,
wait_time_sec)
time.sleep(0.1)
elif (params.camera_ioc_prefix == '2bmbSP1:'):
wait_time_sec = float(params.num_white_images) * float(
params.exposure_time) + 60.0
global_PVs['Cam1_NumImages'].put(int(params.num_white_images))
global_PVs['Cam1_Acquire'].put(DetectorAcquire, wait=True,
timeout=5.0) # it was 1000.0
# time.sleep(0.1)
if aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle,
wait_time_sec) == False: # adjust wait time
global_PVs['Cam1_Acquire'].put(DetectorIdle)
log.info(' *** White Fields: Done!')
def checkclose_hdf(global_PVs, params):
buffer_queue = global_PVs['HDF1_QueueSize'].get(
) - global_PVs['HDF1_QueueFree'].get()
# wait_on_hdd = 10
frate = 55.0
wait_on_hdd = buffer_queue / frate + 10
# wait_on_hdd = (global_PVs['HDF1_QueueSize'].get() - global_PVs['HDF1_QueueFree'].get()) / 55.0 + 10
log.info(' *** Buffer Queue (frames): %d ' % buffer_queue)
log.info(' *** Wait HDD (s): %f' % wait_on_hdd)
if aps2bm.wait_pv(
global_PVs["HDF1_Capture_RBV"], 0, wait_on_hdd
) == False: # needs to wait for HDF plugin queue to dump to disk
global_PVs["HDF1_Capture"].put(0)
log.info(' *** File was not closed => forced to close')
log.info(' *** before %d' % global_PVs["HDF1_Capture_RBV"].get())
aps2bm.wait_pv(global_PVs["HDF1_Capture_RBV"], 0, 5)
log.info(' *** after %d' % global_PVs["HDF1_Capture_RBV"].get())
if (global_PVs["HDF1_Capture_RBV"].get() == 1):
log.error(
' *** ERROR HDF FILE DID NOT CLOSE; add_theta will fail')
def init(global_PVs, params):
if (params.camera_ioc_prefix == '2bmbPG3:'):
log.info(' *** init Point Grey camera')
global_PVs['Cam1_TriggerMode'].put('Internal', wait=True) #
global_PVs['Cam1_TriggerMode'].put(
'Overlapped', wait=True
) # sequence Internal / Overlapped / internal because of CCD bug!!
global_PVs['Cam1_TriggerMode'].put('Internal', wait=True) #
global_PVs['Proc1_Filter_Callbacks'].put('Every array')
global_PVs['Cam1_ImageMode'].put('Single', wait=True)
global_PVs['Cam1_Display'].put(1)
global_PVs['Cam1_Acquire'].put(DetectorAcquire)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorAcquire, 2)
global_PVs['Proc1_Callbacks'].put('Disable')
global_PVs['Proc1_Filter_Enable'].put('Disable')
global_PVs['HDF1_ArrayPort'].put('PG3')
log.info(' *** init Point Grey camera: Done!')
elif (params.camera_ioc_prefix == '2bmbSP1:'):
log.info(' ')
log.info(' *** init FLIR camera')
log.info(' *** *** set detector to idle')
global_PVs['Cam1_Acquire'].put(DetectorIdle)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle, 2)
log.info(' *** *** set detector to idle: Done')
# global_PVs['Proc1_Filter_Callbacks'].put( 'Every array', wait=True) # commented out to test if crash (ValueError: invalid literal for int() with base 0: 'Single') still occurs
time.sleep(2)
log.info(' *** *** set trigger mode to Off')
global_PVs['Cam1_TriggerMode'].put('Off', wait=True) #
log.info(' *** *** set trigger mode to Off: done')
time.sleep(7)
log.info(' *** *** set image mode to single')
global_PVs['Cam1_ImageMode'].put(
'Single', wait=True
) # here is where it crashes with (ValueError: invalid literal for int() with base 0: 'Single') Added 7 s delay before
log.info(' *** *** set image mode to single: done')
log.info(' *** *** set cam display to 1')
global_PVs['Cam1_Display'].put(1)
log.info(' *** *** set cam display to 1: done')
log.info(' *** *** set cam acquire')
global_PVs['Cam1_Acquire'].put(DetectorAcquire)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorAcquire, 2)
log.info(' *** *** set cam acquire: done')
if params.station == '2-BM-A':
global_PVs['Cam1_AttributeFile'].put(
'flir2bmaDetectorAttributes.xml')
global_PVs['HDF1_XMLFileName'].put('flir2bmaLayout.xml')
else: # Mona (B-station)
global_PVs['Cam1_AttributeFile'].put(
'flir2bmbDetectorAttributes.xml', wait=True)
global_PVs['HDF1_XMLFileName'].put('flir2bmbLayout.xml', wait=True)
log.info(' *** init FLIR camera: Done!')
def set(global_PVs, params):
fname = params.file_name
# Set detectors
if (params.camera_ioc_prefix == '2bmbPG3:'):
log.info(' ')
log.info(' *** setup Point Grey')
# mona runf always in B with PG camera
global_PVs['Cam1_AttributeFile'].put('monaDetectorAttributes.xml',
wait=True)
global_PVs['HDF1_XMLFileName'].put('monaLayout.xml', wait=True)
global_PVs['Cam1_ImageMode'].put('Multiple')
global_PVs['Cam1_ArrayCallbacks'].put('Enable')
#global_PVs['Image1_Callbacks'].put('Enable')
global_PVs['Cam1_AcquirePeriod'].put(float(params.exposure_time))
global_PVs['Cam1_AcquireTime'].put(float(params.exposure_time))
# if we are using external shutter then set the exposure time
global_PVs['Cam1_FrameRateOnOff'].put(0)
wait_time_sec = int(params.exposure_time) + 5
global_PVs['Cam1_TriggerMode'].put('Overlapped',
wait=True) #Ext. Standard
global_PVs['Cam1_NumImages'].put(1, wait=True)
global_PVs['Cam1_Acquire'].put(DetectorAcquire)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorAcquire, 2)
global_PVs['Cam1_SoftwareTrigger'].put(1)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle, wait_time_sec)
global_PVs['Cam1_Acquire'].put(DetectorAcquire)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorAcquire, 2)
global_PVs['Cam1_SoftwareTrigger'].put(1)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle, wait_time_sec)
log.info(' *** setup Point Grey: Done!')
elif (params.camera_ioc_prefix == '2bmbSP1:'):
log.info(' ')
log.info(' *** setup FLIR camera')
if params.station == '2-BM-A':
global_PVs['Cam1_AttributeFile'].put(
'flir2bmaDetectorAttributes.xml')
global_PVs['HDF1_XMLFileName'].put('flir2bmaLayout.xml')
else: # Mona (B-station)
global_PVs['Cam1_AttributeFile'].put(
'flir2bmbDetectorAttributes.xml', wait=True)
global_PVs['HDF1_XMLFileName'].put('flir2bmbLayout.xml', wait=True)
global_PVs['Cam1_Acquire'].put(DetectorIdle)
aps2bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle, 2)
global_PVs['Cam1_TriggerMode'].put('Off', wait=True)
global_PVs['Cam1_TriggerSource'].put('Line2', wait=True)
global_PVs['Cam1_TriggerOverlap'].put('ReadOut', wait=True)
global_PVs['Cam1_ExposureMode'].put('Timed', wait=True)
global_PVs['Cam1_TriggerSelector'].put('FrameStart', wait=True)
global_PVs['Cam1_TriggerActivation'].put('RisingEdge', wait=True)
global_PVs['Cam1_ImageMode'].put('Multiple')
global_PVs['Cam1_ArrayCallbacks'].put('Enable')
#global_PVs['Image1_Callbacks'].put('Enable')
#global_PVs['Cam1_AcquirePeriod'].put(float(params.exposure_time))
global_PVs['Cam1_FrameRateOnOff'].put(0)
global_PVs['Cam1_AcquireTimeAuto'].put('Off')
global_PVs['Cam1_AcquireTime'].put(float(params.exposure_time))
# if we are using external shutter then set the exposure time
wait_time_sec = int(params.exposure_time) + 5
global_PVs['Cam1_TriggerMode'].put('On', wait=True)
log.info(' *** setup FLIR camera: Done!')
else:
log.error('Detector %s is not defined' % params.camera_ioc_prefix)
return
if fname is None:
log.warning(' *** hdf_writer will not be configured')
else:
_setup_hdf_writer(global_PVs, params, fname)