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neutrons · Jan 13, 2025 · e9becb1 · e9becb1
1 parent 8655c77
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diff --git a/docs/conf.py b/docs/conf.py
@@ -215,6 +215,7 @@ class ExecDirective(Directive):
     Credit goes to:
     https://stackoverflow.com/questions/27875455/displaying-dictionary-data-in-sphinx-documentation/29789910#29789910
     """
+
     has_content = True
 
     def run(self):

diff --git a/docs/drtsans/example_1d.py b/docs/drtsans/example_1d.py
@@ -8,9 +8,9 @@
 # files
 config["mask"] = "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017B_mp/beamstop60_mask_4m.nxs"
 config["flux"] = "/SNS/EQSANS/shared/instrument_configuration/bl6_flux_at_sample"
-config[
-    "sensitivity_file_path"
-] = "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017A_mp/Sensitivity_patched_thinPMMA_4m_79165_event.nxs"
+config["sensitivity_file_path"] = (
+    "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017A_mp/Sensitivity_patched_thinPMMA_4m_79165_event.nxs"
+)
 config["dark_current"] = "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017B_mp/EQSANS_86275.nxs.h5"
 
 # numeric values

diff --git a/notebooks/barscan/biosans_midrange_detector_barscan.ipynb b/notebooks/barscan/biosans_midrange_detector_barscan.ipynb
@@ -15,11 +15,10 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
     "import time\n",
     "\n",
     "# Mantid imports\n",
-    "from mantid.simpleapi import LoadEventNexus, LoadNexusProcessed, SaveNexus, mtd\n",
+    "from mantid.simpleapi import LoadNexusProcessed, mtd\n",
     "\n",
     "# drtsans imports\n",
     "from drtsans.pixel_calibration import calculate_barscan_calibration, load_calibration, as_intensities\n",

diff --git a/notebooks/barscan/biosans_pixel_calibration_22487_with_midrange.ipynb b/notebooks/barscan/biosans_pixel_calibration_22487_with_midrange.ipynb
@@ -23,7 +23,7 @@
     "import numpy as np\n",
     "import os\n",
     "import time\n",
-    "from mantid.simpleapi import LoadEventAsWorkspace2D, LoadNexus, SaveNexus\n",
+    "from mantid.simpleapi import LoadNexus, SaveNexus\n",
     "from drtsans.mono.biosans import calculate_barscan_calibration, as_intensities, plot_detector\n",
     "from drtsans.pixel_calibration import Table\n",
     "\n",
@@ -675,8 +675,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from mantid.simpleapi import LoadEventNexus\n",
-    "from drtsans.mono.biosans import load_calibration, plot_detector\n",
+    "from drtsans.mono.biosans import load_calibration\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\", \"plot_wing_detector\" and \"plot_midrange_detector\" are used to plot both detectors separately\n",
@@ -791,7 +790,7 @@
     "import os\n",
     "import time\n",
     "from mantid.simpleapi import LoadNexus\n",
-    "from drtsans.mono.biosans import calculate_apparent_tube_width, plot_detector\n",
+    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\", \"plot_wing_detector\" and \"plot_midrange_detector\" are used to plot both detectors separately\n",
@@ -900,7 +899,6 @@
    },
    "outputs": [],
    "source": [
-    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "start_time = time.time()\n",
     "calibration_main = calculate_apparent_tube_width(\n",
@@ -996,7 +994,6 @@
     "from mantid.api import mtd\n",
     "from mantid.simpleapi import CreateWorkspace, LoadNexus\n",
     "from drtsans.tubecollection import TubeCollection\n",
-    "from matplotlib import pyplot as plt\n",
     "#\n",
     "# \"plot_histograms\" to create fancy plots of the spectram stored in an input workspace\n",
     "#\n",

diff --git a/notebooks/barscan/biosans_wing_detector_barscan.ipynb b/notebooks/barscan/biosans_wing_detector_barscan.ipynb
@@ -15,11 +15,10 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
     "import time\n",
     "\n",
     "# Mantid imports\n",
-    "from mantid.simpleapi import LoadEventNexus, LoadNexusProcessed, SaveNexus\n",
+    "from mantid.simpleapi import LoadNexusProcessed\n",
     "# drtsans imports\n",
     "from drtsans.pixel_calibration import calculate_barscan_calibration, load_calibration, as_intensities"
    ]

diff --git a/notebooks/biosans/biosans_pixel_calibration_5767.ipynb b/notebooks/biosans/biosans_pixel_calibration_5767.ipynb
@@ -21,7 +21,7 @@
     "import numpy as np\n",
     "import os\n",
     "import time\n",
-    "from mantid.simpleapi import LoadEventAsWorkspace2D, LoadNexus, SaveNexus\n",
+    "from mantid.simpleapi import LoadNexus, SaveNexus\n",
     "from drtsans.mono.biosans import calculate_barscan_calibration, as_intensities, plot_detector\n",
     "from drtsans.pixel_calibration import Table\n",
     "\n",
@@ -562,8 +562,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from mantid.simpleapi import LoadEventNexus\n",
-    "from drtsans.mono.biosans import load_calibration, plot_detector\n",
+    "from drtsans.mono.biosans import load_calibration\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\" and \"plot_wing_detector\" are used to plot both detectors separately\n",
@@ -666,7 +665,7 @@
     "import os\n",
     "import time\n",
     "from mantid.simpleapi import LoadNexus\n",
-    "from drtsans.mono.biosans import calculate_apparent_tube_width, plot_detector\n",
+    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\" and \"plot_wing_detector\" are used to plot both detectors separately\n",
@@ -762,7 +761,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "start_time = time.time()\n",
     "calibration_main = calculate_apparent_tube_width('flood_workspace', component='detector1',\n",
@@ -849,7 +847,6 @@
     "from mantid.api import mtd\n",
     "from mantid.simpleapi import CreateWorkspace, LoadNexus\n",
     "from drtsans.tubecollection import TubeCollection\n",
-    "from matplotlib import pyplot as plt\n",
     "#\n",
     "# \"plot_histograms\" to create fancy plots of the spectram stored in an input workspace\n",
     "#\n",

diff --git a/notebooks/biosans/biosans_pixel_calibration_5767_with_midrange.ipynb b/notebooks/biosans/biosans_pixel_calibration_5767_with_midrange.ipynb
@@ -626,8 +626,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from mantid.simpleapi import LoadEventAsWorkspace2D\n",
-    "from drtsans.mono.biosans import load_calibration, plot_detector\n",
+    "from drtsans.mono.biosans import load_calibration\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\", \"plot_wing_detector\" and \"plot_midrange_detector\" are used to plot both detectors separately\n",
@@ -734,7 +733,7 @@
     "import os\n",
     "import time\n",
     "from mantid.simpleapi import LoadNexus\n",
-    "from drtsans.mono.biosans import calculate_apparent_tube_width, plot_detector\n",
+    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\", \"plot_wing_detector\" and \"plot_midrange_detector\" are used to plot both detectors separately\n",
@@ -767,8 +766,7 @@
    "outputs": [],
    "source": [
     "from drtsans.mono.biosans.simulated_intensities import clone_component_intensities, insert_midrange_detector\n",
-    "from mantid.api import AnalysisDataService\n",
-    "from mantid.simpleapi import mtd, DeleteWorkspace, DeleteWorkspaces, Integration, LoadEventAsWorkspace2D, SaveNexus\n",
+    "from mantid.simpleapi import mtd, DeleteWorkspaces, Integration, SaveNexus\n",
     "import os\n",
     "\n",
     "flood_file = '/HFIR/CG3/IPTS-24666/nexus/CG3_5904.nxs.h5'\n",
@@ -835,7 +833,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "start_time = time.time()\n",
     "calibration_main = calculate_apparent_tube_width(\n",
@@ -929,7 +926,6 @@
     "from mantid.api import mtd\n",
     "from mantid.simpleapi import CreateWorkspace, LoadNexus\n",
     "from drtsans.tubecollection import TubeCollection\n",
-    "from matplotlib import pyplot as plt\n",
     "#\n",
     "# \"plot_histograms\" to create fancy plots of the spectram stored in an input workspace\n",
     "#\n",

diff --git a/notebooks/biosans/biosans_pixel_calibration_838.ipynb b/notebooks/biosans/biosans_pixel_calibration_838.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import os\n",
     "import time\n",
-    "from mantid.simpleapi import LoadEventAsWorkspace2D, LoadNexus\n",
+    "from mantid.simpleapi import LoadNexus\n",
     "from drtsans.mono.biosans import calculate_barscan_calibration, plot_detector\n",
     "\n",
     "#\n",
@@ -204,8 +204,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from mantid.simpleapi import LoadEventAsWorkspace2D\n",
-    "from drtsans.mono.biosans import load_calibration, plot_detector\n",
+    "from drtsans.mono.biosans import load_calibration\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\" and \"plot_wing_detector\" are used to plot both detectors separately\n",
@@ -346,11 +345,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import os\n",
     "import time\n",
     "from mantid.simpleapi import LoadNexus\n",
-    "from drtsans.mono.biosans import calculate_apparent_tube_width, plot_detector\n",
+    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\" and \"plot_wing_detector\" are used to plot both detectors separately\n",

diff --git a/notebooks/biosans/biosans_pixel_calibration_838_midrange.ipynb b/notebooks/biosans/biosans_pixel_calibration_838_midrange.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import os\n",
     "import time\n",
-    "from mantid.simpleapi import LoadEventAsWorkspace2D, LoadNexus,LoadNexusProcessed, Integration, SaveNexus, mtd\n",
+    "from mantid.simpleapi import LoadNexus,LoadNexusProcessed, Integration, mtd\n",
     "from drtsans.mono.biosans import calculate_barscan_calibration, plot_detector\n",
     "from drtsans.mono.biosans.simulated_intensities import clone_component_intensities, insert_midrange_detector\n",
     "#\n",
@@ -267,8 +267,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from mantid.simpleapi import LoadEventNexus\n",
-    "from drtsans.mono.biosans import load_calibration, plot_detector\n",
+    "from drtsans.mono.biosans import load_calibration\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\", \"plot_wing_detector\" and \"plot_midrange_detector\" are used to plot both detectors separately\n",
@@ -421,11 +420,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import os\n",
     "import time\n",
-    "from mantid.simpleapi import LoadNexus\n",
-    "from drtsans.mono.biosans import calculate_apparent_tube_width, plot_detector\n",
+    "from drtsans.mono.biosans import calculate_apparent_tube_width\n",
     "\n",
     "#\n",
     "# \"plot_main_detector\", \"plot_wing_detector\" and \"plot_midrange_detector\" are used to plot both detectors separately\n",

diff --git a/notebooks/gpsans/gpsans_pixel_calibration.ipynb b/notebooks/gpsans/gpsans_pixel_calibration.ipynb
@@ -355,7 +355,6 @@
     "# \"plot_workspace\" is a utility function, which we will use a couple of times\n",
     "#\n",
     "%matplotlib inline\n",
-    "from drtsans.mono.gpsans import plot_detector\n",
     "def plot_workspace(input_workspace, axes_mode='tube-pixel'):\n",
     "    return plot_detector(input_workspace, backend='mpl',axes_mode=axes_mode, imshow_kwargs={})"
    ]
@@ -551,7 +550,6 @@
     "\n",
     "# \"plot_workspace\" is a utility function, which we will use a couple of times\n",
     "%matplotlib inline\n",
-    "from drtsans.mono.gpsans import plot_detector\n",
     "def plot_workspace(input_workspace, axes_mode='tube-pixel'):\n",
     "    return plot_detector(input_workspace, backend='mpl',axes_mode=axes_mode, imshow_kwargs={})"
    ]
@@ -668,7 +666,6 @@
     "#\n",
     "# \"plot_workspace\" is a utility function, which we will use a couple of times\n",
     "#\n",
-    "from drtsans.mono.gpsans import plot_detector\n",
     "def plot_workspace(input_workspace, axes_mode='tube-pixel'):\n",
     "    return plot_detector(input_workspace, backend='mpl',axes_mode=axes_mode, imshow_kwargs={})"
    ]
@@ -908,7 +905,6 @@
     "#\n",
     "# \"plot_workspace\" is a utility function, which we will use a couple of times\n",
     "#\n",
-    "from drtsans.mono.gpsans import plot_detector\n",
     "def plot_workspace(input_workspace, axes_mode='tube-pixel'):\n",
     "    return plot_detector(input_workspace, backend='mpl',axes_mode=axes_mode, imshow_kwargs={})"
    ]

diff --git a/notebooks/gpsans/gpsans_pixel_calibration_9905.ipynb b/notebooks/gpsans/gpsans_pixel_calibration_9905.ipynb
@@ -558,7 +558,6 @@
     "#\n",
     "# \"plot_workspace\" is a utility function, which we will use a couple of times\n",
     "#\n",
-    "from drtsans.mono.gpsans import plot_detector\n",
     "def plot_workspace(input_workspace, axes_mode='tube-pixel'):\n",
     "    return plot_detector(input_workspace, backend='mpl',axes_mode=axes_mode, imshow_kwargs={})"
    ]
@@ -686,7 +685,6 @@
    "source": [
     "import numpy as np\n",
     "from drtsans.tubecollection import TubeCollection\n",
-    "from matplotlib import pyplot as plt\n",
     "\n",
     "#\n",
     "# \"plot_histograms\" to create fancy plots of the spectram stored in an input workspace\n",
@@ -798,7 +796,6 @@
     "#\n",
     "# \"plot_workspace\" is a utility function, which we will use a couple of times\n",
     "#\n",
-    "from drtsans.mono.gpsans import plot_detector\n",
     "def plot_workspace(input_workspace, axes_mode='tube-pixel'):\n",
     "    return plot_detector(input_workspace, backend='mpl',axes_mode=axes_mode, imshow_kwargs={})"
    ]

diff --git a/notebooks/gpsans/gpsans_reduction_1config.ipynb b/notebooks/gpsans/gpsans_reduction_1config.ipynb
@@ -52,7 +52,7 @@
     "from pprint import pprint as pretty_print\n",
     "import time\n",
     "from drtsans.mono.gpsans import (load_all_files, reduce_single_configuration, plot_reduction_output,\n",
-    "                                 reduction_parameters, update_reduction_parameters, validate_reduction_parameters)"
+    "                                 reduction_parameters, update_reduction_parameters)"
    ]
   },
   {
@@ -194,7 +194,7 @@
     "from pprint import pprint as pretty_print\n",
     "import time\n",
     "from drtsans.mono.gpsans import (load_all_files, reduce_single_configuration, plot_reduction_output,\n",
-    "                                 reduction_parameters, update_reduction_parameters, validate_reduction_parameters)"
+    "                                 update_reduction_parameters)"
    ]
   },
   {

diff --git a/notebooks/tubewidth/gpsans_tubewidth.ipynb b/notebooks/tubewidth/gpsans_tubewidth.ipynb
@@ -14,8 +14,6 @@
    "outputs": [],
    "source": [
     "# Standard imports\n",
-    "import os\n",
-    "import sys\n",
     "import time\n",
     "\n",
     "# Third-party packages\n",
@@ -26,10 +24,9 @@
     "# Mantid imports\n",
     "from mantid.simpleapi import LoadEventNexus, Rebin, CreateWorkspace\n",
     "from mantid.api import mtd\n",
-    "from mantid import plots\n",
     "\n",
     "# drtsans imports\n",
-    "from drtsans.pixel_calibration import calculate_apparent_tube_width, load_calibration, as_intensities\n",
+    "from drtsans.pixel_calibration import calculate_apparent_tube_width, load_calibration\n",
     "from drtsans.plots import plot_detector\n",
     "from drtsans.tubecollection import TubeCollection"
    ]

diff --git a/scripts/common_utils.py b/scripts/common_utils.py
@@ -1,4 +1,5 @@
 """ Common utility functions for all SANS """
+
 import os
 import numpy as np
 import matplotlib.pyplot as plt

diff --git a/scripts/examples/plot_wavelength.py b/scripts/examples/plot_wavelength.py
@@ -1,6 +1,7 @@
 """
 Example script to plot the before and after k-correction data for a given slice and frame.
 """
+
 import glob
 import os
 from pathlib import Path

diff --git a/scripts/jupyter_notebooks/gpsans_spice_prepare_sensitivities_template.py b/scripts/jupyter_notebooks/gpsans_spice_prepare_sensitivities_template.py
@@ -8,6 +8,7 @@
 
 
 """
+
 import os
 import warnings
 from drtsans.mono.gpsans.prepare_sensitivities_correction import SpiceRun

diff --git a/scripts/prepare_sensitivities_biosans.py b/scripts/prepare_sensitivities_biosans.py
@@ -1,6 +1,7 @@
 """
     Sensitivities preparation script for Bio-SANS (CG3)
 """
+
 from drtsans.mono.biosans.prepare_sensitivities_correction import PrepareSensitivityCorrection
 
 import os

diff --git a/scripts/prepare_sensitivities_gpsans.py b/scripts/prepare_sensitivities_gpsans.py
@@ -1,6 +1,7 @@
 """
     Sensitivities preparation script for GP-SANS (CG2)
 """
+
 from drtsans.prepare_sensivities_correction import PrepareSensitivityCorrection
 
 

diff --git a/scripts/test_help/biosans_synthetic_sensitivity_dataset.py b/scripts/test_help/biosans_synthetic_sensitivity_dataset.py
@@ -9,6 +9,7 @@
 the Midrange Detector. See Fixture ``biosans_synthetic_sensitivity_dataset`` for detailed use
 
 """
+
 # local imports
 from drtsans.load import __monitor_counts
 from drtsans.mono.biosans.simulated_intensities import clone_component_intensities, insert_midrange_detector

diff --git a/src/drtsans/absolute_units.py b/src/drtsans/absolute_units.py
@@ -3,6 +3,7 @@
 Divide          <https://docs.mantidproject.org/nightly/algorithms/Divide-v1.html>
 Multiply        <https://docs.mantidproject.org/nightly/algorithms/Multiply-v1.html>
 """
+
 from mantid.simpleapi import DeleteWorkspace, Divide, Multiply, mtd
 from mantid.dataobjects import WorkspaceSingleValue
 

diff --git a/src/drtsans/frame_mode.py b/src/drtsans/frame_mode.py
@@ -5,5 +5,6 @@ class FrameMode(Enum):
     r"""
     Selects if instrument operating in frame-skipping mode
     """
+
     not_skip = 0
     skip = 1
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,7 @@ @@
     """
     import os
     import warnings
     from drtsans.mono.gpsans.prepare_sensitivities_correction import SpiceRun
@@ Expand Down @@