diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 3e4d29c52420758b101a2167720f61a32c8acf78..7ef8ce2bc61ea1f6a6563bee9ea8cfed4bb6919e 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -566,9 +566,6 @@
"# Retrieve calibration constants to RAM\n",
"agipd_corr.allocate_constants(modules, (3, mem_cells_db, 512, 128))\n",
"\n",
- "when = {}\n",
- "cons_data = {}\n",
- "variant = {}\n",
"step_timer.start()\n",
"agipd_cal = AGIPD_CalibrationData(\n",
" detector_name=karabo_id,\n",
@@ -595,9 +592,11 @@
"if agipd_corr.corr_bools.get('xray_corr'):\n",
" gain_constants += agipd_cal.illuminated_calibrations\n",
"\n",
+ "# First retrieve dark constants\n",
"agipd_metadata = agipd_cal.metadata(dark_constants)\n",
"if gain_constants:\n",
- " # Gain constants doesn't have gain_mode condition.\n",
+ " # Then retrieve gain constants without\n",
+ " # using the `gain_mode` condition.\n",
" agipd_cal.gain_mode = None\n",
" try:\n",
" illum_metadata = agipd_cal.metadata(gain_constants)\n",
@@ -672,16 +671,14 @@
" (int, dict, str): Module index, {constant name: creation time}, Karabo DA\n",
" \"\"\"\n",
" const_data = dict()\n",
- " when = dict()\n",
- "\n",
+ " variant = dict()\n",
" for cname, mdata in agipd_metadata[da].items():\n",
- " when[cname] = mdata[\"begin_validity_at\"]\n",
" dataset = mdata[\"dataset\"]\n",
" with h5py.File(agipd_cal.caldb_root / mdata[\"path\"], \"r\") as cf: # noqa\n",
" const_data[cname] = np.copy(cf[f\"{dataset}/data\"])\n",
" variant[cname] = cf[dataset].attrs[\"variant\"] if cf[dataset].attrs.keys() else 0 # noqa\n",
- " agipd_corr.init_constants(const_data, when, mod, variant)\n",
- " return module, when, da\n",
+ " agipd_corr.init_constants(const_data, mod, variant)\n",
+ " return module, da\n",
"\n",
"step_timer.start()\n",
"with multiprocessing.Pool(processes=len(modules)) as pool:\n",
@@ -695,22 +692,23 @@
"metadata": {},
"outputs": [],
"source": [
- "# if the yml file contains \"retrieved-constants\", that means a leading\n",
- "# notebook got processed and the reporting would be generated from it.\n",
- "fst_print = True\n",
+ "# Store timestamps for Offset, SlopesPC, and SlopesFF\n",
+ "# in YAML file for time-summary table.\n",
"timestamps = {}\n",
"\n",
- "for i, (modno, when, k_da) in enumerate(const_out):\n",
+ "for mod, mod_mdata in agipd_metadata.items():\n",
+ " modno = int(mod[-2:])\n",
"\n",
" module_timestamps = {}\n",
"\n",
" # Store few time stamps if exists\n",
" # Add NA to keep array structure\n",
" for key in ['Offset', 'SlopesPC', 'SlopesFF']:\n",
- " if key in when and when[key]:\n",
- " module_timestamps[key] = when[key]\n",
+ " if key in mod_mdata:\n",
+ " module_timestamps[key] = mod_mdata[key][\"begin_validity_at\"]\n",
" else:\n",
" module_timestamps[key] = \"NA\"\n",
+ "\n",
" timestamps[module_index_to_qm(modno)] = module_timestamps\n",
"\n",
"seq = sequences[0] if sequences else 0\n",
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index a99d5589f1a6f89f9c007f0a31ac86a6a5abe962..42ba25db41e2de4bf531b3c965c8df066f54d45d 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -478,20 +478,6 @@ class AgipdCorrections:
self.corr_bools.get('blc_hmatch'),
self.corr_bools.get('blc_stripes')]
- self.dark_constants = {"Offset", "Noise", "BadPixelsDark"}
- if not self.gain_mode:
- self.dark_constants.add("ThresholdsDark")
-
- self.gain_constants = set()
- if any(self.pc_bools):
- self.gain_constants |= {"SlopesPC", "BadPixelsPC"}
- if self.corr_bools.get("xray_corr"):
- self.gain_constants |= {"SlopesFF", "BadPixelsFF"}
-
- self.all_constants = self.dark_constants.copy()
- self.all_constants |= self.gain_constants
-
-
def read_file(self, i_proc: int, file_name: str,
apply_sel_pulses: Optional[bool] = True
) -> int:
@@ -1139,7 +1125,7 @@ class AgipdCorrections:
fletcher32=True)
def init_constants(
- self, cons_data: dict, when: dict, module_idx: int, variant: dict):
+ self, cons_data: dict, module_idx: int, variant: dict):
"""
For CI derived gain, a mean multiplication factor of 4.48 compared
to medium gain is used, as no reliable CI data for all memory cells
@@ -1178,8 +1164,6 @@ class AgipdCorrections:
rel_low gain = _rel_medium gain * 4.48
:param cons_data: A dictionary for each retrieved constant value.
- :param when: A dictionary for the creation time
- of each retrieved constant.
:param module_idx: A module_idx index
:param variant: A dictionary for the variant of each retrieved CCV.
:return:
@@ -1190,19 +1174,19 @@ class AgipdCorrections:
calgs_opts = dict(num_threads=os.cpu_count() // len(self.offset))
calgs.transpose_constant(
- self.offset[module_idx], cons_data['Offset'], **calgs_opts)
+ self.offset[module_idx], cons_data["Offset"], **calgs_opts)
# In case noise wasn't retrieved no need for transposing.
- if 'Noise' in cons_data:
+ if "Noise" in cons_data:
calgs.transpose_constant(
- self.noise[module_idx], cons_data['Noise'], **calgs_opts)
+ self.noise[module_idx], cons_data["Noise"], **calgs_opts)
if (
self.gain_mode is AgipdGainMode.ADAPTIVE_GAIN and
- 'ThresholdsDark' in cons_data
+ "ThresholdsDark" in cons_data
):
calgs.transpose_constant(self.thresholds[module_idx],
- cons_data['ThresholdsDark'][..., :3],
+ cons_data["ThresholdsDark"][..., :3],
**calgs_opts)
if self.corr_bools.get("low_medium_gap"):
@@ -1213,12 +1197,12 @@ class AgipdCorrections:
bpixels = cons_data["BadPixelsDark"].astype(np.uint32)
if self.corr_bools.get("xray_corr"):
- if when.get("BadPixelsFF"):
+ if "BadPixelsFF" in cons_data:
bpixels |= cons_data["BadPixelsFF"].astype(np.uint32)[...,
:bpixels.shape[2], # noqa
None]
- if when.get("SlopesFF"): # Checking if constant was retrieved
+ if "SlopesFF" in cons_data: # Checking if constant was retrieved
slopesFF = cons_data["SlopesFF"]
# This could be used for backward compatibility
@@ -1258,7 +1242,7 @@ class AgipdCorrections:
# add additional bad pixel information
if any(self.pc_bools):
- if when.get("BadPixelsPC"):
+ if "BadPixelsPC" in cons_data:
bppc = np.moveaxis(cons_data["BadPixelsPC"].astype(np.uint32),
0, 2)
bpixels |= bppc[..., :bpixels.shape[2], None]
@@ -1266,7 +1250,7 @@ class AgipdCorrections:
# calculate relative gain from the constants
rel_gain = np.ones((128, 512, self.max_cells, 3), np.float32)
- if when.get("SlopesPC"):
+ if "SlopesPC" in cons_data:
slopesPC = cons_data["SlopesPC"].astype(np.float32, copy=False)
# This will handle some historical data in a different format
@@ -1360,28 +1344,6 @@ class AgipdCorrections:
return
- def validate_constants_availability(
- self, const_data: dict, karabo_da: str,
- ) -> bool :
- """
- Validate the constants availability and raise/warn correspondingly.
- Validation is False, if dark constants are not retrieved.
- """
- missing_dark_constants = self.dark_constants - set(const_data)
- missing_gain_constants = self.gain_constants - set(const_data)
-
- if missing_gain_constants:
- warning(
- f"Gain constants {missing_gain_constants} are"
- f" not retrieved for {karabo_da}")
-
- if missing_dark_constants:
- warning(f"Dark constants {missing_dark_constants} are not available"
- f" to correct {karabo_da}")
- return False
- else:
- return True
-
def allocate_constants(self, modules, constant_shape):
"""
Allocate memory for correction constants