Merge pull request #344 from Kvieta1990/master

Major update to Mantid interface

Author: Kvieta1990

addie/config.json

@@ -29,7 +29,6 @@
       "max": 40,
       "delta": 0.02
     },
-    "reduction_configuration_file": "",
     "characterization_file": ""
   },
   "bragg": {

addie/main.py

@@ -131,6 +131,9 @@ class MainWindow(QMainWindow):
     intermediate_grouping = copy.deepcopy(grouping_dict)
     output_grouping = copy.deepcopy(grouping_dict)
 
+    advanced_dict = {'push_bkg': False,
+                     'ele_size': "1.0"}
+
     statusbar_display_time = 5000  # 5s
 
     # external ui (use to make sure there is only one open at a time

addie/processing/mantid/launch_reduction.py

@@ -1,65 +1,8 @@
 import os
-import traceback
-from mantidqt.utils.asynchronous import AsyncTask
+import json
 
 from addie.processing.mantid.master_table.master_table_exporter import TableFileExporter as MantidTableExporter
 
-# Mantid Total Scattering integration
-# (https://github.com/neutrons/mantid_total_scattering)
-try:
-    import total_scattering
-    print("Mantid Total Scattering Version: ", total_scattering.__version__)
-    from total_scattering.reduction.total_scattering_reduction import TotalScatteringReduction
-    MANTID_TS_ENABLED = True
-except ImportError:
-    print('total_scattering module not found. Functionality disabled')
-    MANTID_TS_ENABLED = False
-
-
-class JobPool(object):
-    task_output = None,
-    running = None
-    task_exc_type, task_exc, task_exc_stack = None, None, None
-
-    def __init__(self, configurations):
-        self.jobs = []
-        for config in configurations:
-            print("CONFIG:", config)
-            self.jobs.append(AsyncTask(TotalScatteringReduction, args=(config,),
-                                       success_cb=self.on_success, error_cb=self.on_error,
-                                       finished_cb=self.on_finished))
-
-    def _start_next(self):
-        if self.jobs:
-            self.running = self.jobs.pop(0)
-            self.running.start()
-        else:
-            self.running = None
-
-    def start(self):
-        if not self.jobs:
-            raise RuntimeError('Cannot start empty job list')
-        self._start_next()
-
-    def on_success(self, task_result):
-        # TODO should emit a signal
-        self.task_output = task_result.output
-        print('SUCCESS!!! {}'.format(self.task_output))
-
-    def on_error(self, task_result):
-        # TODO should emit a signal
-        print('ERROR!!!')
-        self.task_exc_type = task_result.exc_type
-        self.task_exc = task_result.exc_value
-        self.task_exc_stack = traceback.extract_tb(task_result.stack)
-        traceback.print_tb(task_result.stack)
-        print(task_result)
-
-    def on_finished(self):
-        '''Both success and failure call this method afterwards'''
-        # TODO should emit a signal
-        self._start_next()  # kick off the next one in the pool
-
 
 def run_mantid(parent):
     num_rows = parent.processing_ui.h3_table.rowCount()
@@ -87,28 +30,56 @@ def run_mantid(parent):
             filename = os.path.join(os.path.expanduser('~'),'.mantid' ,'JSON_output',dictionary['Title'] +'_'+ str(row) + '.json')
             exporter.export(filename,row)
             print("Row",row,"Successfully output to",filename)
-
-    # append the individual rows to input list (reduction_inputs)
-    reduction_inputs = []
-    for row in range(num_rows):
-        if not exporter.isActive(row):
-            print('skipping row {} - inactive'.format(row + 1))  # REMOVE?
-            continue
-        print('Will be running row {} for reduction'.format(row + 1))  # TODO should be debug logging
-        json_input = exporter.retrieve_row_info(row)[0]
-        reduction_input = exporter.convert_from_row_to_reduction(json_input)
-        if not reduction_input:
-            return
-        reduction_inputs.append(reduction_input)
-    if len(reduction_inputs) == 0:
-        print('None of the rows were activated')
-        return
-
-    # locate total scattering script
-    if MANTID_TS_ENABLED:
-        pool = JobPool(reduction_inputs)
-        pool.start()
-    else:
-        # TODO should be on the status bar
-        print('total_scattering module not found. Functionality disabled')
-        return
+            with open(filename) as json_file:
+                data_tmp = json.load(json_file)
+            dict_out_tmp = {}
+            container_type=""
+            for key, item in data_tmp.items():
+                if "Sample" in key:
+                    sample_tmp = {}
+                    for key_s, item_s in item.items():
+                        if "Density" not in key_s:
+                            if "Material" in key_s:
+                                string_tmp = item_s.replace("(", "").replace(")", "")
+                                sample_tmp[key_s] = string_tmp
+                            else:
+                                sample_tmp[key_s] = item_s
+                            if "Geometry" in key_s:
+                                known_shape = ["PAC03", "PAC06", "PAC08",
+                                               "PAC10", "QuartzTube03"]
+                                if item_s["Shape"] in known_shape:
+                                    shape_tmp = "Cylinder"
+                                    container_type = item_s["Shape"]
+                                else:
+                                    shape_tmp = item_s["Shape"]
+                                geo_dict_tmp = {}
+                                for key_tmp in item_s:
+                                    geo_dict_tmp[key_tmp] = item_s[key_tmp]
+                                geo_dict_tmp["Shape"] = shape_tmp
+                                sample_tmp[key_s] = geo_dict_tmp
+                        else:
+                            sample_tmp["MassDensity"] = float(item_s["MassDensity"])
+                    dict_out_tmp[key] = sample_tmp
+                elif "Normalization" in key or "Normalisation" in key:
+                    van_tmp = {}
+                    for key_v, item_v in item.items():
+                        if "Density" not in key_v:
+                            if "Material" in key_v:
+                                string_tmp = item_v.replace("(", "").replace(")", "")
+                                van_tmp[key_v] = string_tmp
+                            else:
+                                van_tmp[key_v] = item_v
+                        else:
+                            van_tmp["MassDensity"] = float(item_v["MassDensity"])
+                    dict_out_tmp[key] = van_tmp
+                else:
+                    dict_out_tmp[key] = item
+            if container_type:
+                dict_out_tmp["Environment"] = { "Name": "InAir",
+                                                "Container": container_type}
+            filename_to_run = os.path.join(os.path.expanduser('~'),'.mantid' ,'JSON_output', 'running_tmp.json')
+            with open(filename_to_run, 'w') as outfile:
+                json.dump(dict_out_tmp, outfile, indent=2)
+            _script_to_run = "bash /SNS/NOM/shared/scripts/mantidtotalscattering/run_mts.sh " + filename_to_run
+            parent.launch_job_manager(job_name='MantidTotalScattering',
+                                      script_to_run=_script_to_run)

addie/processing/mantid/make_calibration_handler/make_calibration.py

@@ -3,7 +3,6 @@
 from qtpy.QtWidgets import (QMainWindow, QComboBox, QFileDialog, QHBoxLayout, QLabel, QDateEdit, QLineEdit, QPushButton,
                             QTableWidgetItem, QVBoxLayout, QWidget)
 from addie.utilities import load_ui
-from addie.widgets.filedialog import get_save_file
 from qtpy import QtCore
 
 import datetime
@@ -34,7 +33,7 @@ def __init__(self, parent=None):
 
 class MakeCalibrationWindow(QMainWindow):
 
-    table_column_width = [60, 250, 350, 350, 90, 300]
+    table_column_width = [60, 250, 600, 90, 300]
     table_row_height = 85
     entry_level =  0
 
@@ -49,9 +48,6 @@ class MakeCalibrationWindow(QMainWindow):
                                                  "calibration_value",
                                                  "calibration_browser",
                                                  "calibration_browser_value",
-                                                 "vanadium_value",
-                                                 "vanadium_browser",
-                                                 "vanadium_browser_value",
                                                  "date",
                                                  "output_dir_browser",
                                                  "output_dir_value",
@@ -175,17 +171,6 @@ def get_run_number_from_nexus_file_name(self, base_nexus_name=''):
             return result.group(1)
         return None
 
-    def vanadium_browser_clicked(self, entry=""):
-        sample_type = "Vanadium"
-        value_ui = self.master_list_ui[entry].vanadium_browser_value
-
-        [_file, run_number] = self._general_browser_clicked(sample_type=sample_type,
-                                                            value_ui=value_ui)
-        if _file:
-            self.master_list_value[entry]["vanadium_browser"] = _file
-            self.master_list_ui[entry].vanadium_value.setText(str(run_number))
-            self.check_run_calibration_status()
-
     def calibration_browser_clicked(self, entry=""):
         sample_type = "Calibration"
         value_ui = self.master_list_ui[entry].calibration_browser_value
@@ -273,41 +258,14 @@ def __insert_new_row(self, row=-1):
         col1_widget.setLayout(verti_layout)
         self.ui.tableWidget.setCellWidget(row, col, col1_widget)
 
-        # new column - Vanadium
-        col = 3
-        # first row
-        # first row
-        label = QLabel("Run #:")
-        vana_value = QLineEdit("")
-        vana_value.returnPressed.connect(lambda entry=_name: self.run_entered(entry))
-        vana_browser_button = QPushButton("Browse...")
-        vana_browser_button.setMinimumWidth(button_width)
-        vana_browser_button.setMaximumWidth(button_width)
-        vana_browser_button.clicked.connect(lambda state, entry=_name:  self.vanadium_browser_clicked(entry))
-        first_row = QHBoxLayout()
-        first_row.addWidget(label)
-        first_row.addWidget(vana_value)
-        first_row.addWidget(vana_browser_button)
-        first_row_widget = QWidget()
-        first_row_widget.setLayout(first_row)
-        # second row
-        vana_browser_button_value = QLabel("N/A")
-
-        verti_layout = QVBoxLayout()
-        verti_layout.addWidget(first_row_widget)
-        verti_layout.addWidget(vana_browser_button_value)
-        col1_widget = QWidget()
-        col1_widget.setLayout(verti_layout)
-        self.ui.tableWidget.setCellWidget(row, col, col1_widget)
-
         # new column - date
-        col = 4
+        col = 3
         date = QDateEdit()
         date.setDate(self.master_date_value)
         self.ui.tableWidget.setCellWidget(row, col, date)
 
         # new column - output dir
-        col = 5
+        col = 4
         browser_button = QPushButton("Browse...")
         browser_button.setMinimumWidth(button_width)
         browser_button.setMaximumWidth(button_width)
@@ -329,18 +287,13 @@ def __insert_new_row(self, row=-1):
                                            calibration_value=cali_value,
                                            calibration_browser=cali_browser_button,
                                            calibration_browser_value=cali_browser_button_value,
-                                           vanadium_value=vana_value,
-                                           vanadium_browser=vana_browser_button,
-                                           vanadium_browser_value=vana_browser_button_value,
                                            date=date,
                                            output_dir_browser=browser_button,
                                            output_dir_value=browser_value,
                                            output_reset=reset)
         self.master_list_ui[_name] = list_local_ui
 
-        list_local_name = dict(vanadium_run_number="",
-                               vanadium_browser="",
-                               calibration_run_number="",
+        list_local_name = dict(calibration_run_number="",
                                calibration_browser="")
         self.master_list_value[_name] = list_local_name
 
@@ -359,10 +312,6 @@ def _check_status_of_row(self, row=-1):
         if not self._check_local_column(run_value = local_list_ui.calibration_value):
             return False
 
-        # Vanadium column
-        if not self._check_local_column(run_value=local_list_ui.vanadium_value):
-            return False
-
         # output dir
         browse_label = local_list_ui.output_dir_value
         if browse_label.text() == 'N/A':
@@ -395,15 +344,37 @@ def check_run_calibration_status(self):
         self.ui.run_calibration_button.setEnabled(_status)
 
     def run_calibration_button_clicked(self):
-        # make dictionary of all infos
+        instr_dict = {"NOM": "NOMAD",
+                      "PG3": "PG3}"}
         o_dict = MakeCalibrationDictionary(parent=self)
-        _file, _ = get_save_file(parent=self,
-                                 caption="Select where and name of json file to create...",
-                                 # directory = '/SNS/users/ntm/',
-                                 filter={'json (*.json)':'json'})
-        if _file:
-            with open(_file, 'w') as fp:
-                simplejson.dump(o_dict.dictionary, fp, indent=2, ignore_nan=True)
+        for calibrant in o_dict.dictionary['Calibrants'].keys():
+            calib_tmp_dict = o_dict.dictionary['Calibrants'][calibrant]
+            calib_file = calib_tmp_dict['Filename']
+            calib_date = calib_tmp_dict['Date'].replace("_", "-")
+            calib_senv = calib_tmp_dict['SampleEnvironment']
+            calib_outd = calib_tmp_dict['CalDirectory']
+            if "/" in calib_file:
+                instrument_name = calib_file.split("/")[2]
+            else:
+                instrument_name = calib_file.split("_")[0]
+            calib_control_file = os.path.join('/SNS/', instrument_name,
+                                              'shared/CALIBRATION/Group_calib_scripts',
+                                              'control_' + calibrant + ".dat")
+            with open(calib_control_file, "w") as calib_f:
+                calib_f.write("{0:<25s}:: {1:s}\n".format("diamond file", calib_file))
+                calib_f.write("{0:<25s}:: {1:s}\n".format("instrument",
+                                                          instr_dict[instrument_name]))
+                calib_f.write("{0:<25s}:: {1:s}\n".format("date", calib_date))
+                calib_f.write("{0:<25s}:: {1:s}\n".format("sample environment",
+                                                          calib_senv))
+                calib_f.write("{0:<25s}:: {1:s}\n".format("output directory",
+                                                          calib_outd))
+            running_script = os.path.join('/SNS/', instrument_name,
+                                          'shared/CALIBRATION/Group_calib_scripts',
+                                          'running')
+            running_script += (" " + calib_control_file)
+            self.parent.launch_job_manager(job_name='MakeCalibration',
+                                           script_to_run=running_script)
 
     def closeEvent(self, c):
         self.parent.make_calibration_ui = None
@@ -452,15 +423,6 @@ def built_dict(self):
             else:
                 cali_filename = None
 
-            # vanadium run number
-            vana_run_number = str(local_list_ui.vanadium_value.text())
-
-            # vanadium full file name (if any)
-            if str(local_list_ui.vanadium_browser.text()) != "N/A":
-                vana_filename = str(local_list_value["vanadium_browser"])
-            else:
-                vana_filename = None
-
             # local date
             _date = local_list_ui.date.date()
             [year, month, day] = _date.getDate()
@@ -472,14 +434,7 @@ def built_dict(self):
             # local output dir
             local_output_dir = str(local_list_ui.output_dir_value.text())
 
-            # save data in vanadium dict
-            vanadium_dict = {}
-            vanadium_dict["RunNumber"] = vana_run_number
-            if vana_filename:
-                vanadium_dict["Filename"] = vana_filename
-
             cali_dict = {}
-            cali_dict["Vanadium"] = vanadium_dict
             if cali_filename:
                 cali_dict["Filename"] = cali_filename