From 01c52bc8c0103410319ebb1976ae86500160eca3 Mon Sep 17 00:00:00 2001
From: Egor Sobolev <egor.sobolev@xfel.eu>
Date: Fri, 26 Aug 2022 12:19:24 +0200
Subject: [PATCH] Apply suggestions
Co-authored-by: Thomas Kluyver <thomas.kluyver@xfel.eu>
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 6 +--
src/cal_tools/agipdlib.py | 49 +++++--------------
2 files changed, 15 insertions(+), 40 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index e1940696b..2048c87e6 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -88,7 +88,7 @@
"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",
"\n",
- "use_litframe_finder = 'auto' # Process only illuminated frames: 'off' - disable, 'device' - use online device data, 'offline' - use offline algorithm, 'auto' - choose online/offline source automatically (default)\n",
+ "use_litframe_finder = 'off' # Process only illuminated frames: 'off' - disable, 'device' - use online device data, 'offline' - use offline algorithm, 'auto' - choose online/offline source automatically (default)\n",
"litframe_device_id = '' # Device ID for a lit frame finder device, empty string to auto detection\n",
"energy_threshold = -1000 # The low limit for the energy (uJ) exposed by frames subject to processing. If -1000, selection by pulse energy is disabled\n",
"\n",
@@ -452,7 +452,7 @@
"outputs": [],
"source": [
"if use_litframe_finder != 'off':\n",
- " from extra_redu import make_litframe_finder\n",
+ " from extra_redu import make_litframe_finder, SourceNotFound as RequiredSourceNotFound\n",
" from extra_redu.litfrm.utils import litfrm_run_report\n",
"\n",
" if use_litframe_finder not in ['auto', 'offline', 'online']:\n",
@@ -482,7 +482,7 @@
" ).format(frmintf=frmintf, trsintf=trsintf, **rec)\n",
" )\n",
" cell_sel = LitFrameSelection(r, train_ids, max_pulses, energy_threshold)\n",
- " except Exception as err:\n",
+ " except RequiredSourceNotFound as err:\n",
" print(\"Cannot use AgipdLitFrameFinder due to:\")\n",
" print(err)\n",
" cell_sel = CellRange(max_pulses, max_cells=mem_cells)\n",
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 852be0440..3da303837 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -1002,50 +1002,25 @@ class AgipdCorrections:
# Only select data corresponding to selected pulses
# and overwrite data in shared-memory leaving
# the required indices to correct
- # - data
- arr = data_dict['data'][:n_img][can_calibrate]
- data_dict['data'][:n_img_sel] = arr
- # - rawgain`
- arr = data_dict['rawgain'][:n_img][can_calibrate]
- data_dict['rawgain'][:n_img_sel] = arr
- # - cellId
- arr = data_dict['cellId'][:n_img][can_calibrate]
- data_dict['cellId'][:n_img_sel] = arr
- # - pulseId
- arr = data_dict['pulseId'][:n_img][can_calibrate]
- data_dict['pulseId'][:n_img_sel] = arr
- # - trainId
- arr = data_dict['trainId'][:n_img][can_calibrate]
- data_dict['trainId'][:n_img_sel] = arr
-
- # arrays generated after reading and initial selection
- # - gain
- arr = data_dict['gain'][:n_img][can_calibrate]
- data_dict['gain'][:n_img_sel] = arr
+ array_names = ["data", "rawgain", "cellId", "pulseId", "trainId", "gain"]
+ # if AGIPD in fixed gain mode or melting snow was not requested
+ # `t0_rgain` and `raw_data` will be empty shared_mem arrays
is_adaptive = self.gain_mode is AgipdGainMode.ADAPTIVE_GAIN
melt_snow = self.corr_bools.get("melt_snow")
if (is_adaptive and melt_snow):
- # - t0_rgain
- arr = data_dict['t0_rgain'][:n_img][can_calibrate]
- data_dict['t0_rgain'][:n_img_sel] = arr
- # - raw_gain
- arr = data_dict['raw_data'][:n_img][can_calibrate]
- data_dict['raw_data'][:n_img_sel] = arr
+ array_names += ["t0_rgain", "raw_data"]
# if baseline correction was not requested
# `msk` and `rel_corr` will still be empty shared_mem arrays
if any(self.blc_bools):
- # - blShift
- arr = data_dict['blShift'][:n_img][can_calibrate]
- data_dict['blShift'][:n_img_sel] = arr
- # - msk
- arr = data_dict['msk'][:n_img][can_calibrate]
- data_dict['msk'][:n_img_sel] = arr
- # - rel_corr
+ array_names += ["blShift", "msk"]
if hasattr(self, "rel_gain"):
- arr = data_dict['rel_corr'][:n_img][can_calibrate]
- data_dict['rel_corr'][:n_img_sel] = arr
+ array_names.append("rel_corr")
+
+ for name in array_names:
+ arr = data_dict[name][:n_img][can_calibrate]
+ data_dict[name][:n_img_sel] = arr
# Overwrite number of images
data_dict['nImg'][0] = n_img_sel
@@ -1628,7 +1603,7 @@ class LitFrameSelection(CellSelection):
litfrmdata: 'AgipdLitFrameFinderOffline',
train_ids: List[int],
crange: Optional[List[int]] = None,
- energy_threshold: Optional[float] = None):
+ energy_threshold: float = -1000):
"""Initialize lit frame selection
:param litfrmdata: AgipdLitFrameFinder output data
@@ -1639,7 +1614,7 @@ class LitFrameSelection(CellSelection):
# read AgipdLitFrameFinder data
self.dev = litfrmdata.meta.litFrmDev
self.crange = validate_selected_pulses(crange, self.ncell_max)
- self.ethr = energy_threshold
+ self.energy_threshold = energy_threshold
nfrm = litfrmdata.output.nFrame
litfrm_train_ids = litfrmdata.meta.trainId
--
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