diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 442f0d65e6b338125d96a4eb47fce961ca45b3f5..5ef0c5b28f63a598a4809547edaf703e47c9eeb5 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -89,6 +89,9 @@
"low_medium_gap = False # 5 sigma separation in thresholding between low and medium gain\n",
"round_photons = False # Round to absolute number of photons, only use with gain corrections\n",
"\n",
+ "# Additional processing\n",
+ "count_lit_pixels = False # Count the number of pixels registering photons\n",
+ "\n",
"# Optional auxiliary devices\n",
"use_ppu_device = '' # Device ID for a pulse picker device to only process picked trains, empty string to disable\n",
"ppu_train_offset = 0 # When using the pulse picker, offset between the PPU's sequence start and actually picked train\n",
@@ -259,6 +262,7 @@
" corr_bools[\"mask_zero_std\"] = mask_zero_std\n",
" corr_bools[\"low_medium_gap\"] = low_medium_gap\n",
" corr_bools[\"round_photons\"] = round_photons\n",
+ " corr_bools[\"count_lit_pixels\"] = count_lit_pixels\n",
"\n",
"# Many corrections don't apply to fixed gain mode; will explicitly disable later if detected\n",
"disable_for_fixed_gain = [\n",
@@ -532,7 +536,8 @@
"metadata": {},
"outputs": [],
"source": [
- "if round_photons and photon_energy <= 0.0:\n",
+ "photon_energy_warn = None\n",
+ "if photon_energy <= 0.0:\n",
" if use_xgm_device:\n",
" # Try to obtain photon energy from XGM device.\n",
" wavelength_data = dc[use_xgm_device, 'pulseEnergy.wavelengthUsed']\n",
@@ -544,18 +549,57 @@
" photon_energy = (h * c / e) / (wavelength_data.as_single_value(rtol=1e-2) * 1e-6)\n",
" print(f'Obtained photon energy {photon_energy:.3f} keV from {use_xgm_device}')\n",
" except ValueError:\n",
- " warning('XGM source available but photon energy varies greater than 1%, '\n",
- " 'photon rounding disabled!')\n",
- " round_photons = False\n",
+ " photon_energy_warn = 'XGM source available but photon energy varies greater than 1%'\n",
" else:\n",
- " warning('Neither explicit photon energy nor XGM device configured, photon rounding disabled!')\n",
+ " photon_energy_warn = 'Neither explicit photon energy nor XGM device configured'\n",
+ "\n",
+ "rounding_threshold_warn = None\n",
+ "if rounding_threshold <= .0 or 1. <= rounding_threshold:\n",
+ " rounding_threshold_warn = 'Round threshold is out of (0, 1) range. Use standard 0.5 value.'\n",
+ " rounding_threshold = 0.5\n",
+ "\n",
+ "if round_photons:\n",
+ " if photon_energy_warn:\n",
+ " warning(photon_energy_warn + ', photon rounding disabled!')\n",
" round_photons = False\n",
- "elif round_photons:\n",
- " print(f'Photon energy for rounding: {photon_energy:.3f} keV')\n",
+ " else:\n",
+ " print(f'Photon energy for rounding: {photon_energy:.3f} keV')\n",
+ " if rounding_threshold_warn:\n",
+ " warning(rounding_threshold_warn)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "if round_photons:\n",
+ " data_units = 'photon'\n",
+ " litpx_threshold = 1.\n",
+ " if not xray_gain:\n",
+ " litpx_threshold *= 7.\n",
+ "else:\n",
+ " data_units = 'keV'\n",
+ " if photon_energy_warn:\n",
+ " warning(photon_energy_warn, '. Use 12 keV for lit-pixel counter threshold')\n",
+ " litpx_threshold = 12.\n",
+ " else:\n",
+ " litpx_threshold = photon_energy\n",
+ "\n",
+ " if rounding_threshold_warn:\n",
+ " warning(rounding_threshold_warn)\n",
+ "\n",
+ "if not xray_gain:\n",
+ " # convert photon energy to ADU (for AGIPD approx. 1 keV = 7 ADU)\n",
+ " # it looks that rounding to photons can be applied to data in ADU as well\n",
+ " litpx_threshold *= 7.\n",
+ " data_units = 'ADU'\n",
"\n",
- "if round_photons and (rounding_threshold <= .0 or 1. <= rounding_threshold):\n",
- " warning('Round threshould is out of (0, 1) range. Use standard 0.5 value.')\n",
- " rounding_threshold = 0.5"
+ "litpx_threshold *= rounding_threshold\n",
+ "\n",
+ "if count_lit_pixels:\n",
+ " print(f\"Count lit-pixels with signal above {litpx_threshold:.3g} {data_units}\")"
]
},
{
@@ -588,6 +632,7 @@
"agipd_corr.photon_energy = photon_energy\n",
"agipd_corr.rounding_threshold = rounding_threshold\n",
"agipd_corr.cs_mg_adjust = cs_mg_adjust\n",
+ "agipd_corr.litpx_threshold = litpx_threshold\n",
"\n",
"agipd_corr.compress_fields = compress_fields\n",
"if recast_image_data:\n",
@@ -906,6 +951,11 @@
" # Perform image-wise correction\"\n",
" pool.starmap(agipd_corr.gain_correction, imagewise_chunks(img_counts))\n",
" step_timer.done_step(\"Gain corrections\")\n",
+ " \n",
+ " # Peform additional processing\n",
+ " if count_lit_pixels:\n",
+ " pool.starmap(agipd_corr.litpixel_counter, imagewise_chunks(img_counts))\n",
+ " step_timer.done_step(\"Lit-pixel counting\")\n",
"\n",
" # Save corrected data\n",
" pool.starmap(agipd_corr.write_file, [\n",
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 05662d4fa126cca01f9f213668739e99d0b9c62c..7dd310093db6aacd4c4d5cc19fb74855d30cd640 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -582,6 +582,7 @@ class AgipdCorrections:
self.photon_energy = 9.2
self.rounding_threshold = 0.5
self.cs_mg_adjust = 7e3
+ self.litpx_threshold = 42
# Output parameters
self.compress_fields = ['gain', 'mask']
@@ -614,7 +615,8 @@ class AgipdCorrections:
'zero_orange', 'force_hg_if_below',
'force_mg_if_below', 'mask_noisy_adc',
'melt_snow', 'common_mode', 'mask_zero_std',
- 'low_medium_gap', 'round_photons']
+ 'low_medium_gap', 'round_photons',
+ 'count_lit_pixels']
if set(corr_bools).issubset(tot_corr_bools):
self.corr_bools = corr_bools
@@ -1495,10 +1497,49 @@ class AgipdCorrections:
self.shared_dict[i]["valid_trains"] = sharedmem.empty(1024, dtype="u8") # noqa
self.shared_dict[i]["nimg_in_trains"] = sharedmem.empty(1024, dtype="i8") # noqa
+ if self.corr_bools.get("count_lit_pixels"):
+ self.shared_dict[i]["litpx_counter"] = LitPixelCounter(
+ self.shared_dict[i], threshold=self.litpx_threshold)
+
if self.corr_bools.get("round_photons"):
self.shared_hist_preround = sharedmem.empty(len(self.hist_bins_preround) - 1, dtype="i8")
self.shared_hist_postround = sharedmem.empty(len(self.hist_bins_postround) - 1, dtype="i8")
+ def litpixel_counter(self, i_proc: int, first: int, last: int):
+ counter = self.shared_dict[i_proc].get("litpx_counter")
+ if counter:
+ counter.set_num_images(self.shared_dict[i_proc]["nImg"][0])
+ counter.process(slice(first, last))
+
+
+class LitPixelCounter:
+ def __init__(self, data, threshold=0.8):
+ self.data = data
+ for name in ["data", "mask", "cellId", "pulseId", "trainId"]:
+ assert name in data
+
+ self.image = data["data"]
+ self.mask = data["mask"]
+
+ self.threshold = threshold
+ self.max_images = data["data"].shape[0]
+
+ self.num_good_px = sharedmem.full(self.max_images, 0, int)
+ self.num_lit_px = sharedmem.full(self.max_images, 0, int)
+
+ self.num_images = self.max_images
+
+ def set_num_images(self, num_images):
+ self.num_images = num_images
+
+ def process(self, chunk):
+ ix = range(*chunk.indices(self.num_images))
+ for i in ix:
+ mask = self.mask[i] == 0
+ self.num_lit_px[i] = np.sum(
+ self.image[i] > self.threshold, initial=0, where=mask)
+ self.num_good_px[i] = np.sum(mask)
+
def validate_selected_pulses(
max_pulses: List[int], max_cells: int