Add INTER reduce

NDXINTER/reduce.py

@@ -1,41 +1,188 @@
-import os
-import shutil
 import sys
-sys.path.append("/isis/NDXMUSR/user/scripts/autoreduction")
+
+AUTOREDUCTION_DIR = r"/autoreduce/data-archive/NDXINTER/user/scripts/autoreduction"
+sys.path.append(AUTOREDUCTION_DIR)
+
+# import mantid algorithms, numpy and matplotlib
+from mantid.simpleapi import *
+import matplotlib.pyplot as plt
+import numpy as np
 import reduce_vars as web_var
+import os
+import json
+from shutil import copy
+
+instrument='INTER'
+
+# Main funcion that gets called by the reduction
+def main(input_file, output_dir):
+    standard_params = web_var.standard_vars
+    advanced_params = web_var.advanced_vars
+    config['defaultsave.directory'] = output_dir
+
+    # Get the angle
+    angle, input_run = get_angle(input_file)
+    # Parse settings from JSON file
+    json_input = standard_params['path_to_json_settings_file']
+    params = parse_json_settings(json_input, angle)
+
+    # Run reduction
+    alg=AlgorithmManager.create("ReflectometryISISLoadAndProcess")
+    properties = {
+    "InputRunList" : input_run,
+    "FirstTransmissionRunList" : params.first_transmission_run_list,
+    "SecondTransmissionRunList" : params.second_transmission_run_list,
+    "ThetaIn" : angle,
+    "DetectorCorrectionType" : params.detector_correction_type,
+    "MonitorBackgroundWavelengthMin" : params.monitor_background_wavelength_min,
+    "MonitorBackgroundWavelengthMax" : params.monitor_background_wavelength_max,
+    "MonitorIntegrationWavelengthMin" : params.monitor_integration_wavelength_min,
+    "MonitorIntegrationWavelengthMax" : params.monitor_integration_wavelength_max,
+    "WavelengthMin" : params.wavelength_min,
+    "WavelengthMax" : params.wavelength_max,
+    "I0MonitorIndex" : params.i_zero_monitor_index,
+    "AnalysisMode" : params.analysis_mode,
+    "StartOverlap" : params.start_overlap,
+    "EndOverlap" : params.end_overlap,
+    "ScaleRHSWorkspace" : params.scale_rhs_workspace,
+    "TransmissionProcessingInstructions" : params.transmission_processing_instructions,
+    "ProcessingInstructions" : params.processing_instructions
+    }
+    alg.setProperties(properties)
+    alg.execute()
 
-def validate(input_file, output_dir):
+    # Save reduced data as Nexus files
+    OutputWorkspace=alg.getPropertyValue("OutputWorkspace")
+    OutputWorkspaceBinned=alg.getPropertyValue("OutputWorkspaceBinned")
+    SaveNexus(OutputWorkspace, os.path.join(output_dir, OutputWorkspace+".nxs"))
+    SaveNexus(OutputWorkspaceBinned, os.path.join(output_dir, OutputWorkspaceBinned+".nxs"))
+
+    # Save a copy of the .json settings file
+    copy(json_input, output_dir)
+
+def get_angle(input_file):
     """
-    Function to ensure that the files we want to use in reduction exist.
-    Please add any files/directories to the required_files/dirs lists.
+    Get the average angle from logs of motor position
+    :param input_file: The input Nexus file
+    :return: Average (mean) angle from motor position readback
     """
-    print("Running validation")
-    required_files = [input_file]
-    required_dirs = [output_dir]
-    for file_path in required_files:
-        if not os.path.isfile(file_path):
-            raise RuntimeError("Unable to find file: {}".format(file_path))
-    for dir in required_dirs:
-        if not os.path.isdir(dir):
-            raise RuntimeError("Unable to find directory: {}".format(dir))
-    print("Validation successful")
-
+    filename = os.path.basename(input_file)
+    run_str = filename.split("INTER")[1].split(".")[0].strip("0")
+    name=instrument+run_str
+    ws=Load(Filename=name, OutputWorkspace='TOF_'+run_str)
+    # Filter the logs for all angles starting from time 0 and use the average of the returned angles
+    (angle_list, average_angle) = FilterLogByTime(ws, 'Theta', StartTime=0)
+    return average_angle, name
 
-def main(input_file, output_dir):
-    validate(input_file, output_dir)
-
-    # Example of printing some stuff which is captured in autoreduction
-    # output log file 
-    print(web_var)
-    print("input_file = " + str(input_file))
-    print("output_dir = " + str(output_dir))
-
-    # Copy raw data to output dir.
-    # Note this should only be done if raw files are small and for specific
-    # purpose such as testing 
-    shutil.copy(input_file, output_dir)
-
-    # And of course, here and below insert your reduction code!
+def parse_json_settings(json_input, angle):
+    """
+    Get experiment settings and instrument settings from JSON file
+    :param angle: Angle passed in and used to select "per angle defaults"
+    :return: Returns all of the parameters needed to do the reduction
+    """
+    params = INTERParams()
+
+    with open(json_input, "r") as read_file:
+        data = json.load(read_file)
+
+    #========================================================================================
+    # Experiment Settings
+    #========================================================================================
+
+    experimentView = data["experimentView"]
+
+    # Set a string based on what integer value is found
+    if experimentView["analysisModeComboBox"] == 1:
+        params.analysis_mode = "MultiDetectorAnalysis"
+    elif experimentView["analysisModeComboBox"] == 0:
+        params.analysis_mode = "PointDetectorAnalysis"
+    else:
+        raise Exception # If the value isn't 1 or 0 then it isn't valid
+
+    perAngleDefaults = experimentView["perAngleDefaults"]
+    rows = perAngleDefaults["rows"]
+
+    # This looks for the run angle and set other parameters accordingly
+    # Using a tolerance of +-0.5% of the motor readback angle
+    min = angle * 0.995
+    max = angle * 1.005
+    angle_found = False
+    for row in rows:
+        # If the value is within -0.5% to +0.5% it is counted as a match
+        if min <= float(row[0]) <= max:
+            angle_found, params = get_per_angle_defaults_params(row, params)
+            break
+
+    # This is the default case
+    if not angle_found:
+        for row in rows:
+            if row[0] == "":
+                angle_found, params = get_per_angle_defaults_params(row, params)
+                break
+
+    if not angle_found:
+        raise Exception # Excpetion for if neither a pre-defined angle nor the default case are found
+
+    params.start_overlap = experimentView["startOverlapEdit"]
+    params.end_overlap = experimentView["endOverlapEdit"]
+    params.scale_rhs_workspace = experimentView["transScaleRHSCheckBox"]
+
+    #========================================================================================
+    # Instrument Settings
+    #========================================================================================
+
+    instrumentView = data["instrumentView"]
+
+    params.monitor_integration_wavelength_min = instrumentView["monIntMinEdit"]
+    params.monitor_integration_wavelength_max = instrumentView["monIntMaxEdit"]
+    params.monitor_background_wavelength_min = instrumentView["monBgMinEdit"]
+    params.monitor_background_wavelength_max = instrumentView["monBgMaxEdit"]
+    params.wavelength_min = instrumentView["lamMinEdit"]
+    params.wavelength_max = instrumentView["lamMaxEdit"]
+    params.i_zero_monitor_index = instrumentView["I0MonitorIndex"]
+
+    # Set a string based on what integer value is found
+    if instrumentView["detectorCorrectionTypeComboBox"] == 1:
+        params.detector_correction_type = "RotateAroundSample"
+    elif instrumentView["detectorCorrectionTypeComboBox"] == 0:
+        params.detector_correction_type = "VerticalShift"
+    else:
+        raise Exception # If the value isn't 1 or 0 then it isn't valid
+
+    return params
+
+def get_per_angle_defaults_params(row, params):
+    """
+    Get parameters that are dependant on the angle
+    :param row: The row for the angle that has been selected (or the row for the default case if no angle was matched)
+    :return: Returns all of the parameters that are dependant on the angle
+    """
+    angle_found = True
+    params.first_transmission_run_list = instrument+row[1]
+    params.second_transmission_run_list = instrument+row[2]
+    params.transmission_processing_instructions = row[3]
+    # Skipping over parameters that are present in the JSON file but not currently used in the reduction
+    params.processing_instructions = row[8]
+    return angle_found, params
+
+class INTERParams:
+    analysis_mode : str
+    first_transmission_run_list : str
+    second_transmission_run_list : str
+    transmission_processing_instructions : str
+    processing_instructions : str
+    start_overlap : str
+    end_overlap : str
+    scale_rhs_workspace : str
+    monitor_integration_wavelength_min : str
+    monitor_integration_wavelength_max : str
+    monitor_background_wavelength_min : str
+    monitor_background_wavelength_max : str
+    wavelength_min : str
+    wavelength_max : str
+    i_zero_monitor_index : str
+    detector_correction_type : str
 
 if __name__ == "__main__":
-    main("test", "test")
+    main('','')
+

NDXINTER/reduce_vars.py

@@ -1,14 +1,20 @@
 standard_vars = {
-    'example standard var' : [1.0, 2.0, 3.0], # example comment
+    'path_to_json_settings_file' : '/autoreduce/scripts/settings.json'
+    # 'analysis_mode': "MultiDetectorAnalysis",
+    # 'first_transmission_run_list' : "INTER00061705",
+    # 'second_transmission_run_list' : "INTER00061669",
+    # 'transmission_processing_instructions': "76-85",
+    # 'processing_instructions': "80-84",
+    # 'start_overlap' : 10.0,
+    # 'end_overlap' : 12.0
 }
 advanced_vars = {
-    'example advanced var' : '5',
+    # 'monitor_integration_wavelength_min' : 4.0,
+    # 'monitor_integration_wavelength_max' : 10.0,
+    # 'monitor_background_wavelength_min': 17.0,
+    # 'monitor_background_wavelength_max': 18.0,
+    # 'wavelength_min' : 1.5,
+    # 'wavelength_max' : 17.0,
+    # 'i_zero_monitor_index' : 2,
+    # 'detector_correction_type': "VerticalShift"
 }
-variable_help = {
-    'standard_vars' : {
-        'example standard var' : "The list of a, b, c"
-    },
-    'advanced_vars' : {
-        'example advanced var' : "example comment"
-    },
-}