diff --git a/docs/development/how_to_write_xfel_calibrate_notebook_NBC.ipynb b/docs/development/how_to_write_xfel_calibrate_notebook_NBC.ipynb
index 62ae6c8ed5d5f3a307f295b163ff0cf57f01a0e6..608689c65f74eb2d0e20b649db712062552bafbf 100644
--- a/docs/development/how_to_write_xfel_calibrate_notebook_NBC.ipynb
+++ b/docs/development/how_to_write_xfel_calibrate_notebook_NBC.ipynb
@@ -19,7 +19,7 @@
},
{
"cell_type": "code",
- "execution_count": 18,
+ "execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
@@ -56,7 +56,7 @@
},
{
"cell_type": "code",
- "execution_count": 19,
+ "execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
@@ -106,14 +106,14 @@
},
{
"cell_type": "code",
- "execution_count": 20,
+ "execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "The available source to correct for HED_IA1_EPX100-1 are ['HED_IA1_EPX100-1/DET/RECEIVER', 'HED_IA1_EPX100-1/DET/RECEIVER:daqOutput', 'HED_IA1_EPX100-1/DET/CONTROL']\n"
+ "The available source to correct for HED_IA1_EPX100-1 are ['HED_IA1_EPX100-1/DET/CONTROL', 'HED_IA1_EPX100-1/DET/RECEIVER', 'HED_IA1_EPX100-1/DET/RECEIVER:daqOutput']\n"
]
}
],
@@ -153,7 +153,7 @@
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
@@ -188,7 +188,7 @@
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": 5,
"metadata": {},
"outputs": [
{
@@ -232,7 +232,7 @@
},
{
"cell_type": "code",
- "execution_count": 23,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
@@ -240,7 +240,7 @@
"output_type": "stream",
"text": [
"Number of trains to correct is 1000\n",
- "Correcting data: 1.0 s\n"
+ "Correcting data: 0.4 s\n"
]
}
],
@@ -275,14 +275,14 @@
},
{
"cell_type": "code",
- "execution_count": 24,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "Writing corrected data: 1.2 s\n"
+ "Writing corrected data: 0.5 s\n"
]
}
],
@@ -294,15 +294,15 @@
"image_counts = run_dc[instrument_source, \"data.image.pixels\"].data_counts(labelled=False)\n",
"\n",
"step_timer.start()\n",
- "\n",
+ "raw_file = run_dc.files[0] # FileAccess object\n",
"with DataFile(out_file, \"w\") as ofile:\n",
" # Create INDEX datasets.\n",
- " ofile.create_index(run_dc.train_ids, from_file=run_dc.files[0])\n",
+ " ofile.create_index(run_dc.train_ids, from_file=raw_file)\n",
"\n",
" # Create METDATA datasets\n",
" ofile.create_metadata(\n",
" like=run_dc,\n",
- " sequence=run_dc.run_metadata()[\"sequenceNumber\"],\n",
+ " sequence=raw_file.sequence,\n",
" instrument_channels=(f\"{instrument_source}/data\",)\n",
" )\n",
" # Create Instrument section to later add corrected datasets.\n",
@@ -327,7 +327,7 @@
},
{
"cell_type": "code",
- "execution_count": 25,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
@@ -374,7 +374,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.7.6"
+ "version": "3.8.11"
},
"orig_nbformat": 4,
"vscode": {
diff --git a/docs/development/how_to_write_xfel_calibrate_notebook_NBC.md b/docs/development/how_to_write_xfel_calibrate_notebook_NBC.md
index dd050d28cec558eea556468264d54a946912fcd5..f4e2c1f60418e28a3c85e13e4bb7852febe2da49 100644
--- a/docs/development/how_to_write_xfel_calibrate_notebook_NBC.md
+++ b/docs/development/how_to_write_xfel_calibrate_notebook_NBC.md
@@ -100,7 +100,7 @@ print(f"The available source to correct for {karabo_id} are {list(run_dc.all_sou
step_timer = StepTimer()
```
- The available source to correct for HED_IA1_EPX100-1 are ['HED_IA1_EPX100-1/DET/RECEIVER', 'HED_IA1_EPX100-1/DET/RECEIVER:daqOutput', 'HED_IA1_EPX100-1/DET/CONTROL']
+ The available source to correct for HED_IA1_EPX100-1 are ['HED_IA1_EPX100-1/DET/CONTROL', 'HED_IA1_EPX100-1/DET/RECEIVER', 'HED_IA1_EPX100-1/DET/RECEIVER:daqOutput']
## Read operating conditions from RAW data.
@@ -191,7 +191,7 @@ step_timer.done_step('Correcting data')
```
Number of trains to correct is 1000
- Correcting data: 1.0 s
+ Correcting data: 0.4 s
## Writing corrected data
@@ -205,15 +205,15 @@ instrument_source = "HED_IA1_EPX100-1/DET/RECEIVER:daqOutput"
image_counts = run_dc[instrument_source, "data.image.pixels"].data_counts(labelled=False)
step_timer.start()
-
+raw_file = run_dc.files[0] # FileAccess object
with DataFile(out_file, "w") as ofile:
# Create INDEX datasets.
- ofile.create_index(run_dc.train_ids, from_file=run_dc.files[0])
+ ofile.create_index(run_dc.train_ids, from_file=raw_file)
# Create METDATA datasets
ofile.create_metadata(
like=run_dc,
- sequence=run_dc.run_metadata()["sequenceNumber"],
+ sequence=raw_file.sequence,
instrument_channels=(f"{instrument_source}/data",)
)
# Create Instrument section to later add corrected datasets.
@@ -228,7 +228,7 @@ with DataFile(out_file, "w") as ofile:
step_timer.done_step('Writing corrected data')
```
- Writing corrected data: 1.2 s
+ Writing corrected data: 0.5 s
# Plotting results
@@ -249,7 +249,5 @@ plt.show()
```
-
-
diff --git a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
index ec806125d14ad6c1eb0171c5d4d862491c9ab7ee..b7424cb07c6e32c83bb24a08b42d7bcb48073174 100644
--- a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
+++ b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
@@ -122,8 +122,8 @@
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools.tools import (\n",
" calcat_creation_time,\n",
- " write_constants_fragment,\n",
" map_seq_files,\n",
+ " write_constants_fragment,\n",
")\n",
"from XFELDetAna.plotting.heatmap import heatmapPlot\n",
"\n",
@@ -486,12 +486,13 @@
" else: # \"50um\"\n",
" data_stored, gain_stored, mask_stored = data_corr, gain, mask\n",
"\n",
+ " seq_file = dc.files[0] # FileAccess\n",
" with DataFile(out_file, \"w\") as ofile:\n",
" # Create INDEX datasets.\n",
- " ofile.create_index(dc.train_ids, from_file=dc.files[0])\n",
+ " ofile.create_index(dc.train_ids, from_file=seq_file)\n",
" ofile.create_metadata(\n",
" like=dc,\n",
- " sequence=dc.run_metadata()[\"sequenceNumber\"],\n",
+ " sequence=seq_file.sequence,\n",
" instrument_channels=(f\"{corr_data_source}/data\",)\n",
" )\n",
"\n",
diff --git a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
index ee81b4a8da982b1a1325f618f9057ed112ae144a..d9d393e879ce49c017c78f88211d1dfe47fdff5c 100644
--- a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
@@ -686,9 +686,10 @@
" # Create CORR files and add corrected data sections.\n",
" image_counts = seq_dc[instrument_src_kda, \"data.adc\"].data_counts(labelled=False)\n",
"\n",
+ " seq_file = seq_dc.files[0] # FileAccess\n",
" with DataFile(out_file, 'w') as outp_file:\n",
" # Create INDEX datasets.\n",
- " outp_file.create_index(seq_dc.train_ids, from_file=seq_dc.files[0])\n",
+ " outp_file.create_index(seq_dc.train_ids, from_file=seq_file)\n",
"\n",
" # Create Instrument section to later add corrected datasets.\n",
" outp_source = outp_file.create_instrument_source(instrument_src_kda)\n",
@@ -723,7 +724,7 @@
" # Create METDATA datasets\n",
" outp_file.create_metadata(\n",
" like=seq_dc,\n",
- " sequence=seq_dc.run_metadata()[\"sequenceNumber\"],\n",
+ " sequence=seq_file.sequence,\n",
" )\n",
"\n",
" step_timer.done_step(f'Saving data time.')\n",
diff --git a/notebooks/ePix100/Correction_ePix100_NBC.ipynb b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
index bc3a719f39ae39c8a6e2a1228cb51ab48740d75c..8c229d36e30483b2e05c362c977ea11ff1a91ea7 100644
--- a/notebooks/ePix100/Correction_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
@@ -602,13 +602,13 @@
" # Write corrected data.\n",
" with DataFile(out_file, \"w\") as ofile:\n",
" dataset_chunk = ((chunk_size_idim,) + oshape[1:]) # e.g. (1, pixels_x, pixels_y) \n",
- "\n",
+ " seq_file = seq_dc.files[0] # FileAccess\n",
" # Create INDEX datasets.\n",
" ofile.create_index(seq_dc.train_ids, from_file=seq_dc.files[0])\n",
" # Create METDATA datasets\n",
" ofile.create_metadata(\n",
" like=seq_dc,\n",
- " sequence=seq_dc.run_metadata()[\"sequenceNumber\"],\n",
+ " sequence=seq_file.sequence,\n",
" instrument_channels=(f'{instrument_src}/data',)\n",
" )\n",
" # Create Instrument section to later add corrected datasets.\n",
diff --git a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
index 3306fa388ece967b786ac14afacfafb813553755..ece51d23ea9ae3d9d61985df6040881beb56ebc1 100644
--- a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
+++ b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
@@ -613,13 +613,13 @@
" image_counts = seq_dc[instrument_src, \"data.image\"].data_counts(labelled=False)\n",
" dataset_chunk = ((chunk_size_idim,) + corr_arrays[\"pixels\"].shape[1:]) # e.g. (1, pixels_x, pixels_y) \n",
" with DataFile(out_file, 'w') as ofile:\n",
- "\n",
+ " seq_file = seq_dc.files[0]\n",
" # Create INDEX datasets.\n",
- " ofile.create_index(seq_dc.train_ids, from_file=seq_dc.files[0])\n",
+ " ofile.create_index(seq_dc.train_ids, from_file=seq_file)\n",
" # Create METDATA datasets\n",
" ofile.create_metadata(\n",
" like=seq_dc,\n",
- " sequence=seq_dc.run_metadata()[\"sequenceNumber\"],\n",
+ " sequence=seq_file.sequence,\n",
" instrument_channels=(f\"{instrument_src}/data\",)\n",
" )\n",
"\n",
diff --git a/src/cal_tools/tools.py b/src/cal_tools/tools.py
index c72a729bb59a2d0ef14b4c99b2785639b016fd08..d9e5e5f9e420a41dfff546b38e95a5fbd81c7bf8 100644
--- a/src/cal_tools/tools.py
+++ b/src/cal_tools/tools.py
@@ -1065,20 +1065,3 @@ def raw_data_location_string(proposal: str, runs: List[int]):
" a preceding 'p'. Example: 'p900203'")
return f"proposal:{proposal} runs:{' '.join(map(str, runs))}"
-
-
-def extract_sequence_number(f: str):
- """Extract sequence number from input.
- Args:
- f (str): EXDF data filename.
- e.g. /gpfs/exfel/exp/CALLAB/202130/p900203/raw/r9046/RAW-R9046-EPIX01-S00000.h5
- Raises:
- ValueError: Sxxxxx is missing from input file
- Returns:
- int: sequence number.
- """
- match = re.search(r'-S(\d+)', f)
- if match:
- return int(match.group(1))
- else:
- raise ValueError(f"No matching pattern for a sequence in the filename {f}.")
\ No newline at end of file
diff --git a/tests/test_cal_tools.py b/tests/test_cal_tools.py
index 795d9ce97d40970321ec73d018938572d1be7708..577a82a4f57122b6153cd4ef92e5f548a424f1de 100644
--- a/tests/test_cal_tools.py
+++ b/tests/test_cal_tools.py
@@ -13,7 +13,6 @@ from cal_tools.plotting import show_processed_modules
from cal_tools.tools import (
creation_date_file_metadata,
creation_date_train_timestamp,
- extract_sequence_number,
get_dir_creation_date,
get_from_db,
get_pdu_from_db,
@@ -582,14 +581,3 @@ def test_raise_raw_data_location_string():
with pytest.raises(ValueError):
raw_data_location_string("900203", [9008, 9009, 9010])
-
-
-def test_extract_sequence_number():
- seq_num = extract_sequence_number(
- "/gpfs/exfel/exp/CALLAB/202031/p900113/raw/r9983/RAW-R9983-AGIPD00-S00012.h5")
- assert seq_num == 12
-
-
-def test_raise_extract_sequence_number():
- with pytest.raises(ValueError):
- extract_sequence_number("/gpfs/exfel/exp/CALLAB/202031/p900113/raw/r9983")