From 8c5bfd65e812dcdc14f0a3b1fbeae4354b050e28 Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Mon, 11 Apr 2022 14:03:43 +0200
Subject: [PATCH] Expose compressed image fields as parameters in AGIPD correct
---
notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb | 12 +++++++++---
src/cal_tools/agipdlib.py | 8 +++++---
2 files changed, 14 insertions(+), 6 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index a9471792d..1ecab067d 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -33,7 +33,7 @@
"ctrl_source_template = '{}/MDL/FPGA_COMP' # path to control information\n",
"karabo_id_control = \"SPB_IRU_AGIPD1M1\" # karabo-id for control device\n",
"\n",
- "slopes_ff_from_files = \"\" # Path to locally stored SlopesFF and BadPixelsFF constants\n",
+ "slopes_ff_from_files = \"\" # Path to locally stored SlopesFF and BadPixelsFF constants, loaded in precorrection notebook\n",
"\n",
"use_dir_creation_date = True # use the creation data of the input dir for database queries\n",
"cal_db_interface = \"tcp://max-exfl016:8015#8045\" # the database interface to use\n",
@@ -88,11 +88,14 @@
"use_litframe_device = '' # Device ID for a lit frame finder device to only process illuminated frames, empty string to disable\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",
+ "# Output parameters\n",
+ "compress_fields = ['gain', 'mask'] # Datasets in image group to compress.\n",
+ "\n",
"# Plotting parameters\n",
"skip_plots = False # exit after writing corrected files and metadata\n",
"cell_id_preview = 1 # cell Id used for preview in single-shot plots\n",
"\n",
- "# Paralellization parameters\n",
+ "# Parallelization parameters\n",
"chunk_size = 1000 # Size of chunk for image-wise correction\n",
"n_cores_correct = 16 # Number of chunks to be processed in parallel\n",
"n_cores_files = 4 # Number of files to be processed in parallel\n",
@@ -491,7 +494,9 @@
"agipd_corr.cm_dark_fraction = cm_dark_fraction\n",
"agipd_corr.cm_n_itr = cm_n_itr\n",
"agipd_corr.noisy_adc_threshold = noisy_adc_threshold\n",
- "agipd_corr.ff_gain = ff_gain"
+ "agipd_corr.ff_gain = ff_gain\n",
+ "\n",
+ "agipd_corr.compress_fields = compress_fields",
]
},
{
@@ -668,6 +673,7 @@
"\n",
" img_counts = pool.map(agipd_corr.apply_selected_pulses, range(len(file_batch)))\n",
" step_timer.done_step(\"Applying selected cells after common mode correction\")\n",
+ " \n",
" # Perform image-wise correction\"\n",
" pool.starmap(agipd_corr.gain_correction, imagewise_chunks(img_counts))\n",
" step_timer.done_step(\"Gain corrections\")\n",
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 5f0c1d137..cf63be6b5 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -343,6 +343,9 @@ class AgipdCorrections:
self.noisy_adc_threshold = 0.25
self.ff_gain = 1
+ # Output parameters
+ self.compress_fields = ['gain', 'mask']
+
# Shared variables for data and constants
self.shared_dict = []
self.offset = {}
@@ -474,7 +477,6 @@ class AgipdCorrections:
image_fields = [
'trainId', 'pulseId', 'cellId', 'data', 'gain', 'mask', 'blShift',
]
- compress_fields = ['gain', 'mask']
n_img = data_dict['nImg'][0]
if n_img == 0:
@@ -498,7 +500,7 @@ class AgipdCorrections:
# so it's efficient to examine the file structure.
for field in image_fields:
arr = data_dict[field][:n_img]
- if field in compress_fields:
+ if field in self.compress_fields:
# gain/mask compressed with gzip level 1, but not
# checksummed as we would have to implement this.
kw = dict(
@@ -517,7 +519,7 @@ class AgipdCorrections:
# Write the corrected data
for field in image_fields:
- if field in compress_fields:
+ if field in self.compress_fields:
self._write_compressed_frames(
image_grp[field], data_dict[field][:n_img],
)
--
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