diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 3fdf35bc8046786557ac1830639e078f10be5c77..0d9de779b982b7eb85b0b6e07ae6640c5ae00944 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -49,6 +49,7 @@
"max_pulses = [0, 500, 1] # range list [st, end, step] of maximum pulse indices within a train. 3 allowed maximum list input elements.\n",
"mem_cells_db = 0 # set to a value different than 0 to use this value for DB queries\n",
"cell_id_preview = 1 # cell Id used for preview in single-shot plots\n",
+ "integration_time = -1 # integration time, negative values for auto-detection.\n",
"\n",
"# Correction parameters\n",
"blc_noise_threshold = 5000 # above this mean signal intensity now baseline correction via noise is attempted\n",
@@ -140,6 +141,7 @@
" AgipdCorrections,\n",
" get_acq_rate,\n",
" get_gain_mode,\n",
+ " get_integration_time,\n",
" get_gain_setting,\n",
" get_num_cells,\n",
")\n",
@@ -372,7 +374,11 @@
" gain_setting = 0\n",
"\n",
"# Evaluate gain mode (operation mode)\n",
- "gain_mode = get_gain_mode(control_fn, h5path_ctrl)"
+ "gain_mode = get_gain_mode(control_fn, h5path_ctrl)\n",
+ "\n",
+ "# Evaluate integration time\n",
+ "if integration_time < 0:\n",
+ " integration_time = get_integration_time(control_fn, h5path_ctrl)"
]
},
{
@@ -388,6 +394,7 @@
"print(f\"• Acquisition rate: {acq_rate}\")\n",
"print(f\"• Gain setting: {gain_setting}\")\n",
"print(f\"• Gain mode: {gain_mode.name}\")\n",
+ "print(f\"• Integration time: {integration_time}\")\n",
"print(f\"• Photon Energy: {photon_energy}\")"
]
},
@@ -476,17 +483,18 @@
" else:\n",
" # TODO: replace with proper retrieval (as done in pre-correction)\n",
" when = agipd_corr.initialize_from_db(\n",
- " karabo_id,\n",
- " k_da,\n",
- " cal_db_interface,\n",
- " creation_time,\n",
- " mem_cells_db,\n",
- " bias_voltage,\n",
- " photon_energy,\n",
- " gain_setting,\n",
- " acq_rate,\n",
- " mod,\n",
- " False,\n",
+ " karabo_id=karabo_id,\n",
+ " karabo_da=k_da,\n",
+ " cal_db_interface=cal_db_interface,\n",
+ " creation_time=creation_time,\n",
+ " memory_cells=mem_cells_db,\n",
+ " bias_voltage=bias_voltage,\n",
+ " photon_energy=photon_energy,\n",
+ " gain_setting=gain_setting,\n",
+ " acquisition_rate=acq_rate,\n",
+ " integration_time=integration_time,\n",
+ " module_idx=mod,\n",
+ " only_dark=False,\n",
" )\n",
" except Exception as e:\n",
" err = f\"Error: {e}\\nError traceback: {traceback.format_exc()}\"\n",
diff --git a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
index df6dc058d7530ad8c26702615cc775079d6247c1..760e60941d08c91429037188d6d76472918d5648 100644
--- a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
+++ b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
@@ -44,6 +44,7 @@
"photon_energy = 9.2 # photon energy in keV\n",
"max_cells_db_dark = 0 # set to a value different than 0 to use this value for dark data DB queries\n",
"max_cells_db = 0 # set to a value different than 0 to use this value for DB queries\n",
+ "integration_time = -1 # integration time, negative values for auto-detection.\n",
"\n",
"# Correction Booleans\n",
"only_offset = False # Apply only Offset correction. if False, Offset is applied by Default. if True, Offset is only applied.\n",
@@ -161,6 +162,10 @@
"\n",
"# Evaluate gain mode (operation mode)\n",
"gain_mode = agipdlib.get_gain_mode(control_fn, h5path_ctrl)\n",
+ "\n",
+ "# Evaluate integration time\n",
+ "if integration_time < 0:\n",
+ " integration_time = agipblib.get_integration_time(control_fn, h5path_ctrl)\n",
" \n",
"print(f\"Gain setting: {gain_setting}\")\n",
"print(f\"Gain mode: {gain_mode.name}\")\n",
@@ -254,6 +259,7 @@
" gain_mode=gain_mode,\n",
" beam_energy=None,\n",
" only_dark=only_dark,\n",
+ " integration_time=integration_time\n",
" )\n",
"\n",
" # Retrieve multiple constants through an input dictionary\n",
@@ -384,6 +390,7 @@
" print(f\"• Acquisition rate: {acq_rate}\")\n",
" print(f\"• Gain mode: {gain_mode.name}\")\n",
" print(f\"• Gain setting: {gain_setting}\")\n",
+ " print(f\"• Integration time: {integration_time}\")\n",
" print(f\"• Photon Energy: {photon_energy}\")\n",
" print(\"Constant metadata is saved under \\\"retrieved-constants\\\" in calibration_metadata.yml\\n\")"
]
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index 7661d99d8300ce7d9a9a02f211e7d91bc25ca983..35fddcd6ac142b9b73b3d4ee58995b6252623df2 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -101,6 +101,7 @@
" get_bias_voltage,\n",
" get_gain_mode,\n",
" get_gain_setting,\n",
+ " get_integration_time,\n",
" get_num_cells,\n",
")\n",
"from cal_tools.enums import AgipdGainMode, BadPixels\n",
@@ -185,6 +186,13 @@
"else:\n",
" print(f'Something is clearly wrong; slow data indicates gain modes {run_gain_modes}')\n",
"\n",
+ "if integration_time < 0:\n",
+ " integration_times = [get_integration_time(fn, h5path_ctrl) for fn in control_names]\n",
+ " if len(set(integration_times)) > 1:\n",
+ " print(f'WARNING: integration time is not constant across the specified dark runs')\n",
+ "\n",
+ "integration_time = integration_times[0]\n",
+ "\n",
"print(f\"Detector in use is {karabo_id}\")\n",
"print(f\"Instrument {instrument}\")\n",
"print(f\"Detector instance {dinstance}\")"
@@ -254,6 +262,7 @@
"print(f\"Output: {out_folder}\")\n",
"print(f\"Bias voltage: {bias_voltage}V\")\n",
"print(f\"Gain setting: {gain_setting}\")\n",
+ "print(f\"Integration time: {integration_time}\")\n",
"print(f\"Operation mode is {'fixed' if fixed_gain_mode else 'adaptive'} gain mode\")"
]
},
@@ -589,7 +598,8 @@
" bias_voltage=bias_voltage,\n",
" acquisition_rate=acq_rate,\n",
" gain_setting=gain_setting,\n",
- " gain_mode=fixed_gain_mode\n",
+ " gain_mode=fixed_gain_mode,\n",
+ " integration_time=integration_time\n",
")"
]
},
@@ -645,7 +655,7 @@
" print(\"Constants parameter conditions are:\\n\")\n",
" print(f\"• memory_cells: {max_cells}\\n• bias_voltage: {bias_voltage}\\n\"\n",
" f\"• acquisition_rate: {acq_rate}\\n• gain_setting: {gain_setting}\\n\"\n",
- " f\"• gain_mode: {fixed_gain_mode}\\n\"\n",
+ " f\"• gain_mode: {fixed_gain_mode}\\n• integration_time: {integration_time}\\n\"\n",
" f\"• creation_time: {md.calibration_constant_version.begin_at if md is not None else creation_time}\\n\")"
]
},
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb
index f81a26a0df06649f5e847f3fe47d93647e0c2fb0..6d734bf9934e6c6835a897991ad73086b37d0937 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb
@@ -59,7 +59,8 @@
"bias_voltage = 300 # Bias voltage\n",
"acq_rate = 0. # the detector acquisition rate, use 0 to try to auto-determine\n",
"gain_setting = 0.1 # the gain setting, use 0.1 to try to auto-determine\n",
- "photon_energy = 8.05 # photon energy in keV"
+ "photon_energy = 8.05 # photon energy in keV\n",
+ "integration_time = -1 # integration time, negative values for auto-detection."
]
},
{
@@ -83,6 +84,7 @@
" get_acq_rate,\n",
" get_bias_voltage,\n",
" get_gain_setting,\n",
+ " get_integration_time,\n",
" get_num_cells,\n",
")\n",
"from cal_tools.agipdutils_ff import (\n",
@@ -161,6 +163,10 @@
" print(e)\n",
" print(\"Set gain settion to 0\")\n",
" gain_setting = 0\n",
+ "\n",
+ "# Evaluate integration time\n",
+ "if integration_time < 0:\n",
+ " integration_time = get_integration_time(filename, h5path_ctrl)\n",
" \n",
"# Evaluate detector instance for mapping\n",
"instrument = karabo_id.split(\"_\")[0]\n",
@@ -171,7 +177,8 @@
"\n",
"print(f\"Using {creation_time} as creation time\")\n",
"print(f\"Operating conditions are:\\n• Bias voltage: {bias_voltage}\\n• Memory cells: {mem_cells}\\n\"\n",
- " f\"• Acquisition rate: {acq_rate}\\n• Gain setting: {gain_setting}\\n• Photon Energy: {photon_energy}\\n\")"
+ " f\"• Acquisition rate: {acq_rate}\\n• Gain setting: {gain_setting}\\n• Integration time: {integration_time}\\n\"\n",
+ " f\"• Photon Energy: {photon_energy}\\n\")"
]
},
{
@@ -265,7 +272,16 @@
"# set the operating condition\n",
"condition = Conditions.Illuminated.AGIPD(mem_cells, bias_voltage, 9.2,\n",
" pixels_x=512, pixels_y=128, beam_energy=None,\n",
- " acquisition_rate=acq_rate, gain_setting=gain_setting)\n",
+ " acquisition_rate=acq_rate, gain_setting=gain_setting,\n",
+ " integration_time=integration_time)\n",
+ "\n",
+ "# Modify acceptable deviations for integration time condition if and only if\n",
+ "# the integration time is not using the standard value (12).\n",
+ "if integration_time != 12:\n",
+ " for p in condition.parameters:\n",
+ " if p.name == 'Integration Time':\n",
+ " p.lower_deviation = 5\n",
+ " p.upper_deviation = 5\n",
"\n",
"# Retrieve a list of all modules corresponding to processed karabo_das\n",
"db_modules = get_pdu_from_db(karabo_id, karabo_da, Constants.AGIPD.SlopesFF(),\n",
diff --git a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
index 8f7ffe5de01203fd761ee89c91d9e6f5e6042432..75c1a43da968cc286ba748fbbebc35a7c7515d7b 100644
--- a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
+++ b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
@@ -58,6 +58,7 @@
"mem_cells = 0. # number of memory cells used, use 0 to auto-derive\n",
"acq_rate = 0. # the detector acquisition rate, use 0 to try to auto-determine\n",
"gain_setting = 0.1 # gain setting can have value 0 or 1, Default=0.1 for no (None) gain-setting\n",
+ "integration_time = -1 # integration time, negative values for auto-detection.\n",
"\n",
"interlaced = False # assume interlaced data format, for data prior to Dec. 2017\n",
"fit_hook = True # fit a hook function to medium gain slope\n",
@@ -96,7 +97,9 @@
"%matplotlib inline\n",
"\n",
"import XFELDetAna.xfelpyanatools as xana\n",
- "from cal_tools.agipdlib import get_acq_rate, get_gain_setting, get_num_cells\n",
+ "from cal_tools.agipdlib import (\n",
+ " get_acq_rate, get_gain_setting, get_integration_time, get_num_cells\n",
+ ")\n",
"from cal_tools.enums import BadPixels\n",
"from cal_tools.plotting import plot_badpix_3d, show_overview\n",
"from cal_tools.tools import (\n",
@@ -239,7 +242,11 @@
" print(\"Gain setting is not found in the control information\")\n",
" print(\"Data will not be processed\")\n",
" sequences = []\n",
- "print(f\"Gain setting: {gain_setting}\")"
+ "print(f\"Gain setting: {gain_setting}\")\n",
+ "\n",
+ "if integration_time < 0:\n",
+ " integration_time = get_integration_time(control_fname, h5path_ctrl)\n",
+ "print(f\"Integration time: {integration_time}\")"
]
},
{
@@ -584,7 +591,8 @@
" memory_cells=mem_cells,\n",
" bias_voltage=bias_voltage,\n",
" acquisition_rate=acq_rate,\n",
- " gain_setting=gain_setting),\n",
+ " gain_setting=gain_setting,\n",
+ " integration_time=integration_time),\n",
" np.zeros((128, 512, mem_cells, 3)),\n",
" cal_db_interface,\n",
" creation_time=creation_time)\n",
@@ -596,7 +604,8 @@
" memory_cells=mem_cells,\n",
" bias_voltage=bias_voltage,\n",
" acquisition_rate=acq_rate,\n",
- " gain_setting=gain_setting),\n",
+ " gain_setting=gain_setting,\n",
+ " integration_time=integration_time),\n",
" np.zeros((128, 512, mem_cells, 3)),\n",
" cal_db_interface, creation_time=creation_time)\n",
" noises[mod] = np.array(noise.data)\n",
@@ -607,7 +616,8 @@
" memory_cells=mem_cells,\n",
" bias_voltage=bias_voltage,\n",
" acquisition_rate=acq_rate,\n",
- " gain_setting=gain_setting),\n",
+ " gain_setting=gain_setting,\n",
+ " integration_time=integration_time),\n",
" np.zeros((128, 512, mem_cells, 3)),\n",
" cal_db_interface, creation_time=creation_time)\n",
" thresholds[mod] = np.array(threshold.data)"
@@ -1482,6 +1492,7 @@
"print(\"Constants parameter conditions are:\\n\")\n",
"print(f\"• memory_cells: {maxcells}\\n• bias_voltage: {bias_voltage}\\n\"\n",
" f\"• acquisition_rate: {acq_rate}\\n• gain_setting: {gain_setting}\\n\"\n",
+ " f\"• integration_time: {integration_time}\\n\"\n",
" f\"• creation_time: {md.calibration_constant_version.begin_at if md is not None else creation_time}\\n\")"
]
},
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 6c2142442f36ab3fec86f97888fec7bc11bd3166..c5a51c2ec7fac3352e49af77e87861ea2d077cef 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -165,6 +165,24 @@ def get_bias_voltage(fname: str, karabo_id_control: str,
return fin[voltage_path][0]
+def get_integration_time(fname: str, h5path_ctrl: str) -> int:
+ """Read integration time from the FPGA device.
+
+ The integration time is specified as an integer number of clock
+ cycles each spanning ~9ns. The default (and legacy) value is 12.
+
+ :param fname: path to file with control information
+ :param h5path_ctrl: path to control information inside the file
+ :return: integration time
+ """
+ h5path_run = h5path_ctrl.replace('CONTROL/', 'RUN/', 1)
+ h5path_time = f'{h5path_run}/integrationTime/value'
+ with h5py.File(fname, 'r') as fd:
+ if h5path_time in fd:
+ return int(fd[h5path_time][0])
+ return 12
+
+
class AgipdCorrections:
def __init__(
@@ -1311,8 +1329,8 @@ class AgipdCorrections:
creation_time: 'datetime.datetime',
memory_cells: float, bias_voltage: int,
photon_energy: float, gain_setting: float,
- acquisition_rate: float, module_idx: int,
- only_dark: bool = False):
+ acquisition_rate: float, integration_time: int,
+ module_idx: int, only_dark: bool = False):
""" Initialize calibration constants from the calibration database
:param karabo_id: karabo identifier
@@ -1324,6 +1342,7 @@ class AgipdCorrections:
:param photon_energy: photon energy used for CCV conditions
:param gain_setting: gain setting used for CCV conditions
:param acquisition_rate: acquistion rate used for CCV conditions
+ :param integration_time: integration time used for CCV conditions
:param module_idx: module index to save retrieved CCV in sharedmem
:param only_dark: load only dark image derived constants. This
implies that a `calfile` is used to load the remaining
@@ -1377,6 +1396,7 @@ class AgipdCorrections:
photon_energy,
beam_energy=None,
only_dark=only_dark,
+ integration_time=integration_time
)
cons_data, when = self.retrieve_constant_and_time(
diff --git a/src/cal_tools/agipdutils.py b/src/cal_tools/agipdutils.py
index 8cf5b4f375d36437f9ccd4f1332d31f5a52fdd9a..e7cbd4667317e0a543ae865ed7e6d8ecaf33d1c6 100644
--- a/src/cal_tools/agipdutils.py
+++ b/src/cal_tools/agipdutils.py
@@ -20,6 +20,7 @@ def assemble_constant_dict(
beam_energy=None,
only_dark=False,
gain_mode=AgipdGainMode.ADAPTIVE_GAIN,
+ integration_time=None
):
"""
Assemble a dictionary with the iCalibrationDB constant names and
@@ -34,6 +35,7 @@ def assemble_constant_dict(
:param gain_setting: (Float) Gain setting
:param acquisition_rate: (Float) Acquisition rate
:param photon_energy: (Float) Photon energy
+ :param integration_time: (Float) Integration time
:param beam_energy: (Float) Beam Energy
:param only_dark: (Bool) Indicating a retrieval for dark constants only from db
:param gain_mode: Operation mode of the detector (default to adaptive gain)
@@ -49,6 +51,7 @@ def assemble_constant_dict(
"acquisition_rate": acquisition_rate,
"gain_setting": gain_setting,
"gain_mode": gain_mode,
+ "integration_time": integration_time,
"pixels_x": 512,
"pixels_y": 128,
},
diff --git a/tests/test_cal_tools.py b/tests/test_cal_tools.py
index f17a290197ba0d0cb28707350eff07474e10e3ff..a2e14e86642cf67bef19cf27901a6195f703c642 100644
--- a/tests/test_cal_tools.py
+++ b/tests/test_cal_tools.py
@@ -21,6 +21,7 @@ from cal_tools.tools import (
ACQ_RATE = 1.1
BIAS_VOLTAGE = 300
GAIN_SETTING = 0
+INTEGRATION_TIME = 12
MEM_CELLS = 352
PHOTON_ENERGY = 9.2
@@ -357,6 +358,7 @@ def test_initialize_from_db():
photon_energy=PHOTON_ENERGY,
gain_setting=GAIN_SETTING,
acquisition_rate=ACQ_RATE,
+ integration_time=INTEGRATION_TIME,
module_idx=0,
only_dark=False,
)
@@ -375,6 +377,7 @@ def test_initialize_from_db():
creation_time=creation_time,
memory_cells=MEM_CELLS, bias_voltage=BIAS_VOLTAGE,
photon_energy=PHOTON_ENERGY, gain_setting=GAIN_SETTING,
+ integration_time=INTEGRATION_TIME,
acquisition_rate=ACQ_RATE, module_idx=0,
only_dark=False,
)