Merge pull request #321 from neutrons/addie_several_updates

Multiple updates

.github/workflows/actions.yml

@@ -28,7 +28,7 @@ jobs:
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }} 
-          channels: marshallmcdonnell,conda-forge,mantid
+          channels: marshallmcdonnell,conda-forge,mantid,neutrons
 
       - name: Apt install deps
         run: sudo apt-get install xvfb freeglut3-dev libglu1-mesa

addie/autoNOM/make_exp_ini_file_and_run_autonom.py

@@ -27,6 +27,7 @@ def __init__(self, parent=None, folder=None):
         # self.parent = parent.ui
         self.parent = parent.autonom_ui
         self.folder = folder
+        self.script_to_run = "python " + parent._autonom_script + " -l -P " + parent.idl_script_dir
 
     def create(self):
         self.retrieve_metadata()
@@ -208,6 +209,7 @@ def run_auto_nom_script(self):
         _script_to_run = self.script_to_run + self.script_flag
         os.chdir(self.folder)
 
+        print("[LOG] " + _script_to_run)
         # o_gui = Step1GuiHandler(parent=self.parent_no_ui)
         o_gui = Step1GuiHandler(main_window=self.parent_no_ui)
         o_gui.set_main_window_title()

addie/autoNOM/run_step1.py

@@ -73,9 +73,9 @@ def create_auto_folder(self):
 
         self._make_folder(_full_path)
         if self.run_autonom:
-            self.parent.statusbar.showMessage("Created folder: " + _full_path + " and running autoNOM script !")
+            self.parent_no_ui.ui.statusbar.showMessage("Created folder: " + _full_path + " and running autoNOM script !")
         else:
-            self.parent.statusbar.showMessage("Created folder: " + _full_path)
+            self.parent_no_ui.ui.statusbar.showMessage("Created folder: " + _full_path)
 
     def retrieve_last_incremented_index(self, list_folder):
         _list_index = []

addie/calculate_gr/event_handler.py

@@ -7,6 +7,9 @@
 import addie.calculate_gr.edit_sq_dialog
 from addie.calculate_gr.save_sq_dialog_message import SaveSqDialogMessageDialog
 from addie.widgets.filedialog import get_save_file
+from mantid.api import AnalysisDataService
+import mantid.simpleapi as simpleapi
+from pystog import Transformer, FourierFilter
 
 
 def check_widgets_status(main_window, enable_gr_widgets=False):
@@ -217,6 +220,56 @@ def generate_gr_step2(main_window, sq_ws_name_list):
             max_q,
             pdf_filter,
             rho0)
+        if main_window.calculategr_ui.ff_check.checkState() == 2:
+            if rho0 is None:
+                print("WARNING: rho0 is not a float. Necessary for applying meaningful Fourier filter.")
+                return
+            # Fourier filter
+            out_ws_temp = AnalysisDataService.retrieve(sq_ws_name)
+            out_ws_r_temp = AnalysisDataService.retrieve(gr_ws_name)
+            r_in = out_ws_r_temp.readX(0)
+            q_in = out_ws_temp.readX(0)
+            sq_in = out_ws_temp.readY(0)
+            transformer = Transformer()
+            import pystog
+            print("PYSTOG:", pystog.__file__)
+            r_in, gr_in, dg_in = transformer.S_to_G(q_in, sq_in, r_in)
+            ff = FourierFilter()
+            r_cutoff_ff_text = main_window.calculategr_ui.lineEdit_rcutoff.text()
+            try:
+                r_cutoff_ff = float(r_cutoff_ff_text)
+            except ValueError:
+                print("WARNING: rcutoff is not a float. Necessary for applying Fourier filter.")
+                return
+
+            q_ft, sq_ft, q_out, sq_out, r_out, gr_out, dsq_ft, dsq, dgr = ff.G_using_S(
+                r_in,
+                gr_in,
+                q_in,
+                sq_in,
+                r_cutoff_ff,
+                rho=rho0)
+
+            new_sq_wks = sq_ws_name + "_ff_rcutoff_" + r_cutoff_ff_text.replace(".", "p")
+            simpleapi.CreateWorkspace(
+                DataX=q_out,
+                DataY=sq_out,
+                OutputWorkspace=new_sq_wks,
+                NSpec=1,
+                unitX="MomentumTransfer")
+            main_window.calculategr_ui.treeWidget_grWsList.add_sq(new_sq_wks)
+            main_window.calculategr_ui.treeWidget_grWsList._workspaceNameList.append(new_sq_wks)
+            plot_sq(main_window, new_sq_wks, color=None, clear_prev=False)
+            gr_ws_name = main_window._myController.calculate_gr(
+                new_sq_wks,
+                pdf_type,
+                min_r,
+                delta_r,
+                max_r,
+                min_q,
+                max_q,
+                pdf_filter,
+                rho0)
 
         # check whether G(r) is in GofR plot to either update or add new plot
         update = main_window.calculategr_ui.graphicsView_gr.has_gr(gr_ws_name)

addie/initialization/events/postprocessing_tab.py

@@ -15,8 +15,8 @@ def run(main_window=None):
     main_window.postprocessing_ui.pushButton.clicked.connect(main_window.reset_q_range)
     main_window.postprocessing_ui.plazcek_fit_range_max.editingFinished.connect(main_window.check_plazcek_widgets)
     main_window.postprocessing_ui.plazcek_fit_range_min.editingFinished.connect(main_window.check_plazcek_widgets)
-    main_window.postprocessing_ui.hydrogen_no.clicked.connect(main_window.no_hidrogen_clicked)
-    main_window.postprocessing_ui.hydrogen_yes.clicked.connect(main_window.hidrogen_clicked)
+    main_window.postprocessing_ui.hydrogen_no.clicked.connect(main_window.no_hydrogen_clicked)
+    main_window.postprocessing_ui.hydrogen_yes.clicked.connect(main_window.hydrogen_clicked)
     main_window.postprocessing_ui.fourier_filter_from.editingFinished.connect(main_window.check_fourier_filter_widgets)
     main_window.postprocessing_ui.fourier_filter_to.editingFinished.connect(main_window.check_fourier_filter_widgets)
     main_window.postprocessing_ui.run_ndabs_output_file_name.textChanged['QString'].connect(

addie/main.py

@@ -278,6 +278,8 @@ class MainWindow(QMainWindow):
     global_key_value = {}
     align_and_focus_powder_from_files_blacklist = []
 
+    idl_modes = ("idl", "idl_dev")
+
     def __init__(self, parent=None, processing_mode=None):
         """ Initialization
         Parameters
@@ -363,6 +365,16 @@ def __init__(self, parent=None, processing_mode=None):
         # color management
         self._pdfColorManager = PDFPlotManager()
 
+        # IDL config scripts
+        idl_script_dir = "/SNS/NOM/shared/autoNOM/stable/"
+        if self.post_processing == "idl_dev":
+            idl_script_dir = "/SNS/NOM/shared/autoNOM/dev/"
+        self.idl_script_dir = idl_script_dir
+        self._autonom_script = os.path.join(idl_script_dir, "autoNOM.py")
+        self._sum_scans_script = os.path.join(idl_script_dir, "sumscans.py")
+        self._ndabs_script = os.path.join(idl_script_dir, "NDabs.py")
+        self._is_sum_scans_python_checked = False
+
         # Connecting all the widgets
         main_tab_events_handler.run(main_window=self)
         autonom_tab_events_handler.run(main_window=self)
@@ -581,13 +593,13 @@ def check_q_range(self):
         _o_gui = Step2GuiHandler(main_window=self)
         _o_gui.check_gui()
 
-    def hidrogen_clicked(self):
+    def hydrogen_clicked(self):
         o_gui = Step2GuiHandler(main_window=self)
-        o_gui.hidrogen_clicked()
+        o_gui.hydrogen_clicked()
 
-    def no_hidrogen_clicked(self):
+    def no_hydrogen_clicked(self):
         o_gui = Step2GuiHandler(main_window=self)
-        o_gui.no_hidrogen_clicked()
+        o_gui.no_hydrogen_clicked()
 
     def yes_background_clicked(self):
         o_gui = Step2GuiHandler(main_window=self)
@@ -996,7 +1008,8 @@ def main(config=None):
             help='Set processing mode (default=%(default)s)',
             choices=[
                 'mantid',
-                'idl'])
+                'idl',
+                'idl_dev'])
 
         try:  # set up bash completion as a soft dependency
             import argcomplete  # noqa

addie/menu/event_handler.py

@@ -54,7 +54,7 @@ def help_about_clicked(main_window):
 
 
 def activate_reduction_tabs(main_window):
-    if main_window.post_processing == 'idl':
+    if main_window.post_processing in main_window.idl_modes:
         tab_0 = True
         tab_1 = True
         tab_2 = False

addie/menu/file/settings/advanced_file_window.py

@@ -33,15 +33,19 @@ def __init__(self, parent=None):
     def init_widgets(self):
         _idl_status = False
         _mantid_status = False
-        if self.parent.post_processing == 'idl':
+        if self.parent.post_processing in self.parent.idl_modes:
             _idl_status = True
         else:
             _mantid_status = True
 
-        self.ui.idl_groupbox.setVisible(self.parent.advanced_window_idl_groupbox_visible)
+        self.ui.idl_config_group_box.setVisible(self.parent.advanced_window_idl_groupbox_visible)
 
         self.ui.idl_post_processing_button.setChecked(_idl_status)
         self.ui.mantid_post_processing_button.setChecked(_mantid_status)
+        # When 'idl' or 'idl_dev' model is enabled from CLI, this should enable
+        # the setting box, etc. by default without the need for explicitly
+        # clicking on the 'IDL' radio button.
+        self.post_processing_clicked()
 
         instrument = self.parent.instrument["full_name"]
         list_instrument_full_name = self.parent.list_instrument["full_name"]
@@ -58,6 +62,12 @@ def init_widgets(self):
         self.ui.cache_dir_label.setText(self.parent.cache_folder)
         self.ui.output_dir_label.setText(self.parent.output_folder)
 
+        # IDL config
+        self.ui.autonom_path_line_edit.setText(self.parent._autonom_script)
+        self.ui.sum_scans_path_line_edit.setText(self.parent._sum_scans_script)
+        self.ui.ndabs_path_line_edit.setText(self.parent._ndabs_script)
+        self.ui.idl_config_browse_button_dialog = None
+
         self.ui.centralwidget.setContentsMargins(10, 10, 10, 10)
 
     def is_idl_selected(self):
@@ -71,7 +81,7 @@ def post_processing_clicked(self):
             _post = 'mantid'
             _idl_groupbox_visible = False
 
-        self.ui.idl_groupbox.setVisible(_idl_groupbox_visible)
+        self.ui.idl_config_group_box.setVisible(_idl_groupbox_visible)
         self.parent.post_processing = _post
         self.parent.activate_reduction_tabs() # hide or show right tabs
         self.parent.advanced_window_idl_groupbox_visible = _idl_groupbox_visible
@@ -97,5 +107,71 @@ def output_dir_button_clicked(self):
             self.ui.output_dir_label.setText(str(_output_folder))
             self.parent.output_folder = str(_output_folder)
 
+    # IDL Config - Line Edits
+    def autonom_path_line_edited(self):
+        """ update autonom script in top-level after line editing """
+        _script = str(self.ui.autonom_path_line_edit.text())
+        self.parent._autonom_script = _script
+
+    def sum_scans_path_line_edited(self):
+        """ update sum scans script in top-level after line editing """
+        _script = str(self.ui.sum_scans_path_line_edit.text())
+        self.parent._sum_scans_script = _script
+
+    def ndabs_path_line_edited(self):
+        """ update ndabs script in top-level after line editing """
+        _script = str(self.ui.ndabs_path_line_edit.text())
+        self.parent._ndabs_script = _script
+
+    # IDL Config - Browse Buttons
+    def _idl_button_clicked(self, line_edit):
+        """ Utility function to handle IDL script path browse buttons """
+
+        # Initialize with current script in line edit
+        script = str(line_edit.text())
+
+        # Get current working directory to open file dialog in
+        _current_folder = self.parent.current_folder
+
+        # Launch file dialog
+        self.ui.idl_config_browse_button_dialog = QFileDialog(
+            parent=self.ui,
+            directory=_current_folder,
+            caption="Select File",
+            filter=("Python (*.py);; All Files (*.*)"))
+
+        # Handle if we select a file or cancel
+        if self.ui.idl_config_browse_button_dialog.exec_():
+            files = self.ui.idl_config_browse_button_dialog.selectedFiles()
+
+            if files[0] != '':
+                script = str(files[0])
+                line_edit.setText(script)
+
+        # Set the class attribute back to None for monitoring / testing
+        self.ui.idl_config_browse_button_dialog = None
+
+        return script
+
+    def autonom_path_browse_button_clicked(self):
+        """ Handle browse button clicked for autonom script path """
+        line_edit = self.ui.autonom_path_line_edit
+        self.parent._autonom_script = self._idl_button_clicked(line_edit)
+
+    def sum_scans_path_browse_button_clicked(self):
+        """ Handle browse button clicked for sum scans script path """
+        line_edit = self.ui.sum_scans_path_line_edit
+        self.parent._sum_scans_script = self._idl_button_clicked(line_edit)
+
+    def ndabs_path_browse_button_clicked(self):
+        """ Handle browse button clicked for ndabs script path """
+        line_edit = self.ui.ndabs_path_line_edit
+        self.parent._ndabs_script = self._idl_button_clicked(line_edit)
+
+    def sum_scans_python_version_checkbox_toggled(self):
+        """ Handle the sum scans checkbox for using the python version """
+        _is_checked = self.ui.sum_scans_python_version_checkbox.isChecked()
+        self.parent._is_sum_scans_python_checked = _is_checked
+
     def closeEvent(self, c):
         self.parent.advanced_window_ui = None

addie/processing/idl/run_sum_scans.py

@@ -6,13 +6,19 @@
 
 class RunSumScans(object):
 
-    script = 'python  /SNS/NOM/shared/autoNOM/stable/sumscans.py '
     output_file = ''
 
     def __init__(self, parent=None):
         self.parent = parent.ui.postprocessing_ui
         self.parent_no_ui = parent
+        self.o_gui_handler = Step2GuiHandler(main_window=self.parent_no_ui)
         self.folder = os.getcwd()
+        self.set_sum_scans_script()
+
+    def set_sum_scans_script(self):
+        self.script_path = self.o_gui_handler.get_sum_scans_script()
+        self.script = 'python ' + self.script_path
+        print("SumScans: ", self.script)
 
     def run(self):
         self._background = self.collect_background_runs()
@@ -30,12 +36,13 @@ def run_script(self):
         print("[LOG] " + _script_to_run)
 
     def add_script_flags(self):
+        self.set_sum_scans_script()
         _script = self.script
 
         if not self.parent.interactive_mode_checkbox.isChecked():
-            _script += "-n True"
-        if self.parent.pytest.isChecked():
-            _script += "-u True"
+            _script += " -n True "
+        if self.parent_no_ui._is_sum_scans_python_checked:
+            _script += " -u True "
 
         qmax_list = str(self.parent.pdf_qmax_line_edit.text()).strip()
         if not (qmax_list == ""):
@@ -45,9 +52,9 @@ def add_script_flags(self):
 
     def create_output_file(self):
         _output_file_name = "sum_" + self.parent.sum_scans_output_file_name.text() + ".inp"
-#        print("_output_file_name: {}".format(_output_file_name))
+        # print("_output_file_name: {}".format(_output_file_name))
         _full_output_file_name = os.path.join(self.folder, _output_file_name)
- #       print("_full_output_file_name: {}".format(_full_output_file_name))
+        # print("_full_output_file_name: {}".format(_full_output_file_name))
         self.full_output_file_name = _full_output_file_name
 
         f = open(_full_output_file_name, 'w')
@@ -61,7 +68,7 @@ def create_output_file(self):
 
         # hydrogen flag
         plattype_flag = 0
-        if o_gui_handler.is_hidrogen_clicked():
+        if o_gui_handler.is_hydrogen_clicked():
             plattype_flag = 2
         f.write("platype {}\n".format(plattype_flag))
 

addie/processing/idl/step2_gui_handler.py

@@ -34,14 +34,14 @@ def move_to_folder(self):
             self.main_window.current_folder = _new_folder
             self.main_window.setWindowTitle(_new_folder)
 
-    def is_hidrogen_clicked(self):
+    def is_hydrogen_clicked(self):
         return self.main_window.postprocessing_ui.hydrogen_yes.isChecked()
 
-    def hidrogen_clicked(self):
+    def hydrogen_clicked(self):
         _range = self.hidrogen_range
         self.populate_hidrogen_range(_range)
 
-    def no_hidrogen_clicked(self):
+    def no_hydrogen_clicked(self):
         _range = self.no_hidrogen_range
         self.populate_hidrogen_range(_range)
 
@@ -113,6 +113,9 @@ def define_new_output_file_name(self):
             _output_file_name = self.default_ndabs_output_file_name
         return _output_file_name
 
+    def get_sum_scans_script(self):
+        return self.main_window._sum_scans_script
+
     def check_import_export_buttons(self):
         _export_status = False
         if self.main_window.postprocessing_ui.table.rowCount() > 0:

addie/processing/idl/table_handler.py

@@ -90,7 +90,8 @@ def right_click(self, position=None):
         _refresh_table = -1
         _clear_table = -1
         # _import = -1
-        # _export = -1        _check_all = -1
+        # _export = -1
+        _check_all = -1
         _uncheck_all = -1
         _undo = -1
         _redo = -1