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fix algo import
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@mdoucet
mdoucet committed Mar 8, 2024
1 parent 3534eff commit e6243f5
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25 changes: 13 additions & 12 deletions reduction/lr_reduction/event_reduction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import numpy as np

from . import background
from . import DeadTimeCorrection


def get_wl_range(ws):
Expand Down Expand Up @@ -241,22 +242,22 @@ def get_dead_time_correction(self):
tof_min = self._ws_sc.getTofMin()
tof_max = self._ws_sc.getTofMax()

corr_ws = SingleReadoutDeadTimeCorrection(InputWorkspace=self._ws_sc,
DeadTime=self.DEAD_TIME,
TOFStep=self.DEAD_TIME_TOF_STEP,
Paralyzable=self.paralyzable,
TOFRange=[tof_min, tof_max],
OutputWorkspace="corr")
corr_ws = DeadTimeCorrection.call(InputWorkspace=self._ws_sc,
DeadTime=self.DEAD_TIME,
TOFStep=self.DEAD_TIME_TOF_STEP,
Paralyzable=self.paralyzable,
TOFRange=[tof_min, tof_max],
OutputWorkspace="corr")
corr_sc = corr_ws.readY(0)
wl_bins = corr_ws.readX(0) / self.constant

# Direct beam workspace
corr_ws = SingleReadoutDeadTimeCorrection(InputWorkspace=self._ws_db,
DeadTime=self.DEAD_TIME,
TOFStep=self.DEAD_TIME_TOF_STEP,
Paralyzable=self.paralyzable,
TOFRange=[tof_min, tof_max],
OutputWorkspace="corr")
corr_ws = DeadTimeCorrection.call(InputWorkspace=self._ws_db,
DeadTime=self.DEAD_TIME,
TOFStep=self.DEAD_TIME_TOF_STEP,
Paralyzable=self.paralyzable,
TOFRange=[tof_min, tof_max],
OutputWorkspace="corr")
corr_db = corr_ws.readY(0)

# Flip the correction since we are going from TOF to Q
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99 changes: 48 additions & 51 deletions reduction/notebooks/workflow.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@
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Expand Down Expand Up @@ -44,11 +44,11 @@
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Expand All @@ -72,11 +72,11 @@
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Expand All @@ -100,17 +100,18 @@
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"outputs": [],
"source": [
"import importlib\n",
"import lr_reduction\n",
"from lr_reduction import workflow\n",
"from lr_reduction import template\n",
"from lr_reduction import output\n",
Expand All @@ -123,11 +124,11 @@
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Expand Down Expand Up @@ -185,14 +186,14 @@
},
{
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Expand All @@ -201,26 +202,22 @@
"name": "stdout",
"output_type": "stream",
"text": [
"wl=4.25; ths=-0.599733; thi=-0.00812677; No offset\n",
"Background on both sides: [133 135] [148 150]\n",
"Dead time correction: [0.753782 -> 0.938569] at [0.0487517 -> 0.0220792]\n",
"Normalization options: True True\n",
"Template data was passed instead of a file path: template data not saved\n",
"wl=4.25; ths=-1.18271; thi=-0.00812677; No offset\n",
"Background on both sides: [133 135] [148 150]\n",
"Dead time correction: [0.749746 -> 0.92837] at [0.099448 -> 0.0441559]\n",
"Normalization options: True True\n",
"Template data was passed instead of a file path: template data not saved\n",
"wl=4.25; ths=-2.34284; thi=-0.00812677; No offset\n",
"Background on both sides: [131 133] [149 151]\n",
"Dead time correction: [0.753723 -> 0.937186] at [0.194985 -> 0.0865754]\n",
"Normalization options: True True\n",
"Template data was passed instead of a file path: template data not saved\n",
"wl=4.25; ths=-4.63906; thi=-0.00812677; No offset\n",
"Background on both sides: [131 133] [149 151]\n",
"Dead time correction: [0.7496 -> 0.928125] at [0.389949 -> 0.173141]\n",
"Normalization options: True True\n",
"Template data was passed instead of a file path: template data not saved\n"
"wl=4.25; ths=-0.599733; thi=-0.00812677; No offset\n"
]
},
{
"ename": "NameError",
"evalue": "name 'SingleReadoutDeadTimeCorrection' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[6], line 20\u001b[0m\n\u001b[1;32m 18\u001b[0m template_data \u001b[38;5;241m=\u001b[39m template\u001b[38;5;241m.\u001b[39mread_template(template_path, sequence_number)\n\u001b[1;32m 19\u001b[0m template_data\u001b[38;5;241m.\u001b[39mdead_time \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[0;32m---> 20\u001b[0m \u001b[43mworkflow\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mreduce\u001b[49m\u001b[43m(\u001b[49m\u001b[43mws\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtemplate_data\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moutput_dir\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdata_dir\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maverage_overlap\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/git/LiquidsReflectometer/reduction/lr_reduction/workflow.py:29\u001b[0m, in \u001b[0;36mreduce\u001b[0;34m(ws, template_file, output_dir, average_overlap, q_summing, bck_in_q, is_live, functional_background)\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 17\u001b[0m \u001b[38;5;124;03m Function called by reduce_REFL.py, which lives in /SNS/REF_L/shared/autoreduce\u001b[39;00m\n\u001b[1;32m 18\u001b[0m \u001b[38;5;124;03m and is called by the automated reduction workflow.\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[38;5;124;03m along constant-Q lines rather than along TOF/pixel boundaries.\u001b[39;00m\n\u001b[1;32m 27\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 28\u001b[0m \u001b[38;5;66;03m# Call the reduction using the template\u001b[39;00m\n\u001b[0;32m---> 29\u001b[0m qz_mid, refl, d_refl, meta_data \u001b[38;5;241m=\u001b[39m \u001b[43mtemplate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprocess_from_template_ws\u001b[49m\u001b[43m(\u001b[49m\u001b[43mws\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtemplate_file\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 30\u001b[0m \u001b[43m \u001b[49m\u001b[43mq_summing\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mq_summing\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 31\u001b[0m \u001b[43m \u001b[49m\u001b[43mtof_weighted\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mq_summing\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 32\u001b[0m \u001b[43m \u001b[49m\u001b[43mclean\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mq_summing\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 33\u001b[0m \u001b[43m \u001b[49m\u001b[43mbck_in_q\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbck_in_q\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 34\u001b[0m \u001b[43m \u001b[49m\u001b[43mfunctional_background\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfunctional_background\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 35\u001b[0m \u001b[43m \u001b[49m\u001b[43minfo\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 37\u001b[0m \u001b[38;5;66;03m# Save partial results\u001b[39;00m\n\u001b[1;32m 38\u001b[0m coll \u001b[38;5;241m=\u001b[39m output\u001b[38;5;241m.\u001b[39mRunCollection()\n",
"File \u001b[0;32m~/git/LiquidsReflectometer/reduction/lr_reduction/template.py:232\u001b[0m, in \u001b[0;36mprocess_from_template_ws\u001b[0;34m(ws_sc, template_data, q_summing, tof_weighted, bck_in_q, clean, info, normalize, theta_value, ws_db, functional_background)\u001b[0m\n\u001b[1;32m 218\u001b[0m event_refl \u001b[38;5;241m=\u001b[39m event_reduction\u001b[38;5;241m.\u001b[39mEventReflectivity(ws_sc, ws_db,\n\u001b[1;32m 219\u001b[0m signal_peak\u001b[38;5;241m=\u001b[39mpeak, signal_bck\u001b[38;5;241m=\u001b[39mpeak_bck,\n\u001b[1;32m 220\u001b[0m norm_peak\u001b[38;5;241m=\u001b[39mnorm_peak, norm_bck\u001b[38;5;241m=\u001b[39mnorm_bck,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 228\u001b[0m functional_background\u001b[38;5;241m=\u001b[39mfunctional_background,\n\u001b[1;32m 229\u001b[0m instrument\u001b[38;5;241m=\u001b[39mevent_reduction\u001b[38;5;241m.\u001b[39mEventReflectivity\u001b[38;5;241m.\u001b[39mINSTRUMENT_4B)\n\u001b[1;32m 231\u001b[0m \u001b[38;5;66;03m# R(Q)\u001b[39;00m\n\u001b[0;32m--> 232\u001b[0m qz, refl, d_refl \u001b[38;5;241m=\u001b[39m \u001b[43mevent_refl\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mspecular\u001b[49m\u001b[43m(\u001b[49m\u001b[43mq_summing\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mq_summing\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtof_weighted\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtof_weighted\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 233\u001b[0m \u001b[43m \u001b[49m\u001b[43mbck_in_q\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbck_in_q\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mclean\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mclean\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnormalize\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnormalize\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 234\u001b[0m qz_mid \u001b[38;5;241m=\u001b[39m (qz[:\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m] \u001b[38;5;241m+\u001b[39m qz[\u001b[38;5;241m1\u001b[39m:])\u001b[38;5;241m/\u001b[39m\u001b[38;5;241m2.0\u001b[39m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNormalization options: \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m%\u001b[39m (normalize, template_data\u001b[38;5;241m.\u001b[39mscaling_factor_flag))\n",
"File \u001b[0;32m~/git/LiquidsReflectometer/reduction/lr_reduction/event_reduction.py:293\u001b[0m, in \u001b[0;36mEventReflectivity.specular\u001b[0;34m(self, q_summing, tof_weighted, bck_in_q, clean, normalize)\u001b[0m\n\u001b[1;32m 290\u001b[0m \u001b[38;5;66;03m# First, let's compute the dead-time correction if we need it\u001b[39;00m\n\u001b[1;32m 291\u001b[0m \u001b[38;5;66;03m# We do this first because the specular calls below may modify the input workspace\u001b[39;00m\n\u001b[1;32m 292\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdead_time:\n\u001b[0;32m--> 293\u001b[0m dead_time_corr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_dead_time_correction\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 295\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tof_weighted:\n\u001b[1;32m 296\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mspecular_weighted(q_summing\u001b[38;5;241m=\u001b[39mq_summing, bck_in_q\u001b[38;5;241m=\u001b[39mbck_in_q)\n",
"File \u001b[0;32m~/git/LiquidsReflectometer/reduction/lr_reduction/event_reduction.py:244\u001b[0m, in \u001b[0;36mEventReflectivity.get_dead_time_correction\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 241\u001b[0m tof_min \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ws_sc\u001b[38;5;241m.\u001b[39mgetTofMin()\n\u001b[1;32m 242\u001b[0m tof_max \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ws_sc\u001b[38;5;241m.\u001b[39mgetTofMax()\n\u001b[0;32m--> 244\u001b[0m corr_ws \u001b[38;5;241m=\u001b[39m \u001b[43mSingleReadoutDeadTimeCorrection\u001b[49m(InputWorkspace\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ws_sc,\n\u001b[1;32m 245\u001b[0m DeadTime\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mDEAD_TIME,\n\u001b[1;32m 246\u001b[0m TOFStep\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mDEAD_TIME_TOF_STEP,\n\u001b[1;32m 247\u001b[0m Paralyzable\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mparalyzable,\n\u001b[1;32m 248\u001b[0m TOFRange\u001b[38;5;241m=\u001b[39m[tof_min, tof_max],\n\u001b[1;32m 249\u001b[0m OutputWorkspace\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcorr\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 250\u001b[0m corr_sc \u001b[38;5;241m=\u001b[39m corr_ws\u001b[38;5;241m.\u001b[39mreadY(\u001b[38;5;241m0\u001b[39m)\n\u001b[1;32m 251\u001b[0m wl_bins \u001b[38;5;241m=\u001b[39m corr_ws\u001b[38;5;241m.\u001b[39mreadX(\u001b[38;5;241m0\u001b[39m) \u001b[38;5;241m/\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconstant\n",
"\u001b[0;31mNameError\u001b[0m: name 'SingleReadoutDeadTimeCorrection' is not defined"
]
}
],
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19 changes: 14 additions & 5 deletions reduction/test/test_dead_time.py
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import os
import numpy as np
#from lr_reduction.DeadTimeCorrection import SingleReadoutDeadTimeCorrection
from lr_reduction.DeadTimeCorrection import SingleReadoutDeadTimeCorrection

import mantid
import mantid.simpleapi as mtd_api
Expand All @@ -18,8 +18,12 @@ def test_deadtime(nexus_dir):
with amend_config(data_dir=nexus_dir):
ws = mtd_api.Load("REF_L_198409")

corr_ws = SingleReadoutDeadTimeCorrection(InputWorkspace=ws)

algo = SingleReadoutDeadTimeCorrection()
algo.PyInit()
algo.setProperty("InputWorkspace", ws)
algo.setProperty("OutputWorkspace", "dead_time_corr")
algo.PyExec()
corr_ws = algo.getProperty('OutputWorkspace').value
corr = corr_ws.readY(0)
for c in corr:
assert(c>0)
Expand All @@ -33,8 +37,13 @@ def test_deadtime_paralyzable(nexus_dir):
with amend_config(data_dir=nexus_dir):
ws = mtd_api.Load("REF_L_198409")

corr_ws = SingleReadoutDeadTimeCorrection(InputWorkspace=ws,
Paralyzable=True)
algo = SingleReadoutDeadTimeCorrection()
algo.PyInit()
algo.setProperty("InputWorkspace", ws)
algo.setProperty("Paralyzable", True)
algo.setProperty("OutputWorkspace", "dead_time_corr")
algo.PyExec()
corr_ws = algo.getProperty('OutputWorkspace').value
corr = corr_ws.readY(0)
with open("dc.txt", 'w') as fd:
fd.write(str(corr))
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