From 0e330426fe8cf94667bdaefcc76a1095010aae84 Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Tue, 9 Apr 2024 15:31:56 +0200
Subject: [PATCH] Fix small issues and typos from testing
---
.../Characterize_DynamicFF_NBC.ipynb | 27 ++++++++-----------
.../DynamicFF/Correct_DynamicFF_NBC.ipynb | 13 ++++-----
2 files changed, 18 insertions(+), 22 deletions(-)
diff --git a/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb b/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb
index dc41c2ed4..60b07daeb 100644
--- a/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb
+++ b/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb
@@ -22,15 +22,16 @@
"metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"run_high = 1 # run number in which dark data was recorded, required\n",
"run_low = 2 # run number in which flat-field data was recorded, required\n",
- "operation_mode = \"TI_DynamicFF\" # Detector operation mode, optional (defaults to \"TI_DynamicFF\")\n",
+ "operation_mode = \"PCA_DynamicFF\" # Detector operation mode, optional (defaults to \"PCA_DynamicFF\")\n",
"\n",
"# Data files parameters.\n",
"karabo_da = ['-1'] # data aggregators\n",
"karabo_id = \"SPB_MIC_HPVX2\" # karabo prefix of Shimadzu HPV-X2 devices\n",
"\n",
"# Database access parameters.\n",
- "cal_db_interface = \"tcp://max-exfl-cal001:8021\" # calibration DB interface to use\n",
- "db_output = True # if True, the notebook sends dark constants to the calibration database\n",
+ "cal_db_interface = \"tcp://max-exfl-cal001:8021\" # Unused, calibration DB interface to use\n",
+ "cal_db_timeout = 30000 # Unused, calibration DB timeout\n",
+ "db_output = False # if True, the notebook sends dark constants to the calibration database\n",
"local_output = True # if True, the notebook saves dark constants locally\n",
"\n",
"# Calibration constants parameters\n",
@@ -63,10 +64,7 @@
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools.tools import (\n",
" get_dir_creation_date,\n",
- " get_random_db_interface,\n",
- " get_report,\n",
- " save_dict_to_hdf5,\n",
- " run_prop_seq_from_path,\n",
+ " save_dict_to_hdf5\n",
")\n",
"from cal_tools.restful_config import calibration_client\n",
"from cal_tools.shimadzu import ShimadzuHPVX2\n",
@@ -81,16 +79,12 @@
"metadata": {},
"outputs": [],
"source": [
- "cal_db_interface = get_random_db_interface(cal_db_interface)\n",
- "print(f'Calibration database interface: {cal_db_interface}')\n",
- "print()\n",
- "\n",
"cc = calibration_client()\n",
"pdus = cc.get_all_phy_det_units_from_detector(\n",
- " {\"detector_identifier\": karabo_id})\n",
+ " {\"detector_identifier\": karabo_id}) # TODO: Use creation_time for snapshot_at\n",
"\n",
"if not pdus[\"success\"]:\n",
- " raise ValueException(\"Failed to retrieve PDUs\")\n",
+ " raise ValueError(\"Failed to retrieve PDUs\")\n",
"\n",
"detector_info = pdus['data'][0]['detector']\n",
"detector = ShimadzuHPVX2(detector_info[\"source_name_pattern\"])\n",
@@ -117,6 +111,7 @@
" )\n",
"\n",
"constants = {}\n",
+ "\n",
"step_timer = StepTimer()"
]
},
@@ -165,7 +160,7 @@
"\n",
" # process\n",
" step_timer.start()\n",
- " dark = dffc.process_dark(images_dark)\n",
+ " dark = dffc.process_dark(images_dark) # Amounts to a per-pixel mean right now.\n",
"\n",
" # put results in the dict\n",
" module_constants = constants.setdefault(meta[\"db_module\"], {})\n",
@@ -224,8 +219,8 @@
" dark_conditions = constants[meta[\"db_module\"]][\"Offset\"][\"conditions\"]\n",
"\n",
" if conditions != dark_conditions:\n",
- " ValueError(\"The conditions for flat-field run does not match \"\n",
- " \"the dark run conditions. Skip flat-field characterization.\")\n",
+ " raise ValueError(f\"The conditions for flat-field run {conditions}) do not match \"\n",
+ " f\"the dark run conditions ({dark_conditions}). Skip flat-field characterization.\")\n",
"\n",
" key_data = flat_dc[source_name][image_key]\n",
" images_flat = key_data.ndarray()\n",
diff --git a/notebooks/DynamicFF/Correct_DynamicFF_NBC.ipynb b/notebooks/DynamicFF/Correct_DynamicFF_NBC.ipynb
index c3a875eca..e570cdf6d 100644
--- a/notebooks/DynamicFF/Correct_DynamicFF_NBC.ipynb
+++ b/notebooks/DynamicFF/Correct_DynamicFF_NBC.ipynb
@@ -27,7 +27,8 @@
"karabo_id = \"SPB_MIC_HPVX2\" # karabo prefix of Shimadzu HPV-X2 devices\n",
"\n",
"# Database access parameters.\n",
- "cal_db_interface = \"tcp://max-exfl-cal001:8021\" # calibration DB interface to use\n",
+ "cal_db_interface = \"tcp://max-exfl-cal001:8021\" # Unused, calibration DB interface to use\n",
+ "cal_db_timeout = 30000 # Unused, calibration DB timeout\n",
"\n",
"# Correction parameters\n",
"n_components = 20 # number of principal components of flat-field to use in correction\n",
@@ -83,10 +84,10 @@
"\n",
"cc = calibration_client()\n",
"pdus = cc.get_all_phy_det_units_from_detector(\n",
- " {\"detector_identifier\": karabo_id})\n",
+ " {\"detector_identifier\": karabo_id}) # TODO: Use creation_time for snapshot_at\n",
"\n",
"if not pdus[\"success\"]:\n",
- " raise ValueException(\"Failed to retrieve PDUs\")\n",
+ " raise ValueError(\"Failed to retrieve PDUs\")\n",
"\n",
"detector_info = pdus['data'][0]['detector']\n",
"detector = ShimadzuHPVX2(detector_info[\"source_name_pattern\"])\n",
@@ -218,7 +219,7 @@
" # correct and write sequence files\n",
" for seq_id, train_mask in sequence_trains(train_ids, 200):\n",
" step_timer.start()\n",
- " print('* sequience', seq_id)\n",
+ " print('* sequence', seq_id)\n",
" seq_train_ids = train_ids[train_mask]\n",
" seq_timestamps = ts[train_mask]\n",
" dc_seq = dc.select_trains(by_id[seq_train_ids])\n",
@@ -238,8 +239,8 @@
" for da in process_modules:\n",
" instrument_source = modules[da][\"raw_source_name\"]\n",
" keydata = dc_seq[instrument_source][image_key].drop_empty_trains()\n",
- " count = keydata.data_counts()\n",
- " i = np.flatnonzero(count.values)\n",
+ " count = keydata.data_counts(labelled=False)\n",
+ " i = np.flatnonzero(count)\n",
" raw_images = keydata.select_trains(np.s_[i]).ndarray()\n",
"\n",
" # not pulse resolved\n",
--
GitLab