Auto load ST on startup and version bump (#64)

* Open the plugin on startup

* Remove default scanner constraint file

* Add fsleyes layout and launch it on startup

* Add double quotes to strings in the install script

* Fix typo

* Call the function rather than simulate a click

* Add the tests

* Add quadprog

* Add skimage

* bump version

* Add fieldmap test

* Add B0shim tab test

* Create files for tests of specific tabs

* Bump ST version

* Add multiple fieldmap and b0shim tests

* Update files from code review

* Upgrade fsleyes to 1.9.0

* Install prelude in the CI

.github/workflows/tests.yml

@@ -51,6 +51,13 @@ jobs:
         run: |
           echo "$HOME/shimming-toolbox/bin" >> $GITHUB_PATH
 
+      - name: prelude Ubuntu
+        if: contains(matrix.os, 'ubuntu')
+        run: |
+          echo "Download prelude"
+          st_download_data prelude
+          sudo install prelude/prelude /usr/local/bin
+
 #      - name: Run unit tests Mac
 #        if: contains(matrix.os, 'macos')
 #        run: |

fsleyes_plugin_shimming_toolbox/components/dropdown_component.py

@@ -24,14 +24,18 @@ def __init__(self, panel, dropdown_metadata, label, option_name, list_components
                     }
 
             label (str): Label of the button describing the dropdown
-            option_name (str): Name of the options of the dropdown, set to 'no_arg' is not an option
+            option_name (str): Name of the options of the dropdown, start with 'no_arg' if it is not an option
             list_components (list): list of Components
             info_text (str): Info message displayed when hovering over the "i" icon. Leave blank to auto fill using option_name
             cli (function): CLI function used by the dropdown
-            component_to_dropdown_choice (list): Tells which component associates with which dropdown selection. 
-                                                 If None, assumes 1:1. 
+            component_to_dropdown_choice (list): Tells which component associates with which dropdown selection.
+                                                 If None, assumes 1:1.
         """
         super().__init__(panel, list_components)
+
+        self.choice_box_sizer = None
+        self.choice_box = None
+
         self.dropdown_metadata = dropdown_metadata
         self.label = label
         self.info_text = info_text
@@ -98,7 +102,7 @@ def unshow_choice_box_sizers(self):
                 sizer.Show(False)
 
     def create_choice_box(self):
-        self.choice_box = wx.Choice(self.panel, choices=self.dropdown_choices)
+        self.choice_box = wx.Choice(self.panel, choices=self.dropdown_choices, name=self.option_name)
         self.choice_box.Bind(wx.EVT_CHOICE, self.on_choice)
         button = wx.Button(self.panel, -1, label=self.label)
         self.choice_box_sizer = wx.BoxSizer(wx.HORIZONTAL)
@@ -114,7 +118,7 @@ def on_choice(self, event, is_propagating_up=True):
 
             is_propagating_up tells the dropdown to propagate the on_choice() command to the parent drop down until
             there is no more parent. Moreover, on each call of on_choice(), the propagation will also go down. This
-            allows to recalculate each dropdown. THere is some redundency since we would really just want the most
+            allows to recalculate each dropdown. There is some redundancy since we would really just want the most
             parent dropdown to send the down propagation, but this will do for now.
         """
         # Get the selection from the choice box widget
@@ -168,6 +172,6 @@ def find_index(self, label):
         return 0
 
     def create_sizer(self):
-        """Create the a sizer containing tab-specific functionality."""
+        """Create a sizer containing tab-specific functionality."""
         sizer = wx.BoxSizer(wx.VERTICAL)
         return sizer

fsleyes_plugin_shimming_toolbox/components/run_component.py

@@ -14,9 +14,6 @@
 from fsleyes_plugin_shimming_toolbox.events import EVT_RESULT, EVT_LOG
 from fsleyes_plugin_shimming_toolbox.worker_thread import WorkerThread
 
-# Load icon resources
-play_icon = wx.Bitmap(os.path.join(__DIR_ST_PLUGIN_IMG__, 'play.png'), wx.BITMAP_TYPE_PNG)
-
 
 class RunComponent(Component):
     """Component which contains input and run button.
@@ -57,6 +54,7 @@ def add_button_run(self):
         """Add the run button which will call the ``Shimming Toolbox`` CLI."""
         button_run = wx.Button(self.panel, -1, label="Run", size=(85, 48))
         button_run.Bind(wx.EVT_BUTTON, self.button_run_on_click)
+        play_icon = wx.Bitmap(os.path.join(__DIR_ST_PLUGIN_IMG__, 'play.png'), wx.BITMAP_TYPE_PNG)
         button_run.SetBitmap(play_icon, dir=wx.LEFT)
         self.sizer.Add(button_run, 0, wx.CENTRE)
         self.sizer.AddSpacer(10)
@@ -150,6 +148,9 @@ def button_run_on_click(self, event):
         Calls the relevant ``Shimming Toolbox`` CLI command (``st_function``) in a thread
 
         """
+        self.run()
+
+    def run(self):
         if not self.worker:
             try:
                 command, msg = self.get_run_args(self.st_function)
@@ -190,7 +191,7 @@ def get_run_args(self, st_function):
         for component in self.list_components:
             for name, input_text_box_list in component.input_text_boxes.items():
 
-                if name == "no_arg":
+                if name.startswith('no_arg'):
                     continue
 
                 for input_text_box in input_text_box_list:

fsleyes_plugin_shimming_toolbox/st_plugin.py

@@ -18,6 +18,7 @@
 
 import fsleyes.controls.controlpanel as ctrlpanel
 import fsleyes.views.canvaspanel as canvaspanel
+import textwrap
 import wx
 
 from fsleyes_plugin_shimming_toolbox.tabs.b0shim_tab import B0ShimTab
@@ -26,6 +27,15 @@
 from fsleyes_plugin_shimming_toolbox.tabs.fieldmap_tab import FieldMapTab
 from fsleyes_plugin_shimming_toolbox.tabs.mask_tab import MaskTab
 
+STLayout = textwrap.dedent(
+    """
+    fsleyes.views.orthopanel.OrthoPanel
+    layout2|name=OrthoPanel 1;caption=Ortho View 1;state=67376064;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=-1;besth=-1;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|dock_size(5,0,0)=22|
+    fsleyes.controls.orthotoolbar.OrthoToolBar,fsleyes.controls.overlaydisplaytoolbar.OverlayDisplayToolBar,fsleyes.controls.overlaylistpanel.OverlayListPanel,fsleyes.controls.locationpanel.LocationPanel,fsleyes_plugin_shimming_toolbox.st_plugin.STControlPanel;syncLocation=True,syncOverlayOrder=True,syncOverlayDisplay=True,syncOverlayVolume=True,movieRate=400,movieAxis=3;showCursor=True,bgColour=#000000ff,fgColour=#ffffffff,cursorColour=#00ff00ff,cursorGap=False,showColourBar=False,colourBarLocation=top,colourBarLabelSide=top-left,showXCanvas=True,showYCanvas=True,showZCanvas=True,showLabels=True,labelSize=12,layout=horizontal,xzoom=847.0127756479341,yzoom=847.0127756479341,zzoom=100.0
+    layout2|name=Panel;caption=;state=768;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=-1;besth=-1;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|name=OrthoToolBar;caption=Ortho view toolbar;state=67382012;dir=1;layer=10;row=0;pos=0;prop=100000;bestw=572;besth=35;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|name=OverlayDisplayToolBar;caption=Display toolbar;state=67382012;dir=1;layer=11;row=0;pos=0;prop=100000;bestw=953;besth=56;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1;notebookid=-1;transparent=255|name=OverlayListPanel;caption=Overlay list;state=67373052;dir=3;layer=0;row=0;pos=0;prop=100000;bestw=197;besth=80;minw=1;minh=1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=197;floath=99;notebookid=-1;transparent=255|name=LocationPanel;caption=Location;state=67373052;dir=3;layer=0;row=0;pos=1;prop=100000;bestw=391;besth=111;minw=1;minh=1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=391;floath=130;notebookid=-1;transparent=255|name=STControlPanel;caption=Shimming Toolbox;state=67373052;dir=1;layer=0;row=0;pos=0;prop=100000;bestw=600;besth=400;minw=1;minh=1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=600;floath=419;notebookid=-1;transparent=255|dock_size(5,0,0)=22|dock_size(3,0,0)=176|dock_size(1,10,0)=37|dock_size(1,11,0)=58|dock_size(1,0,0)=384|
+    """
+)
+
 
 # We need to create a ctrlpanel.ControlPanel instance so that it can be recognized as a plugin by FSLeyes
 # Class hierarchy: wx.Panel > fslpanel.FSLeyesPanel > ctrlpanel.ControlPanel

fsleyes_plugin_shimming_toolbox/tabs/b0shim_tab.py

@@ -4,7 +4,7 @@
 import os
 import wx
 
-from fsleyes_plugin_shimming_toolbox import __CURR_DIR__, __ST_DIR__
+from fsleyes_plugin_shimming_toolbox import __CURR_DIR__
 from fsleyes_plugin_shimming_toolbox.tabs.tab import Tab
 from fsleyes_plugin_shimming_toolbox.components.dropdown_component import DropdownComponent
 from fsleyes_plugin_shimming_toolbox.components.input_component import InputComponent
@@ -18,6 +18,19 @@
 class B0ShimTab(Tab):
     def __init__(self, parent, title="B0 Shim"):
 
+        self.dropdown_coil_format_rt = None
+        self.dropdown_slice_rt = None
+        self.dropdown_opt_rt = None
+        self.dropdown_scanner_order_rt = None
+        self.dropdown_coil_format_dyn = None
+        self.dropdown_slice_dyn = None
+        self.dropdown_opt_dyn = None
+        self.dropdown_scanner_order_dyn = None
+        self.choice_box = None
+        self.run_component_mi = None
+        self.run_component_rt = None
+        self.run_component_dyn = None
+
         description = "Perform B0 shimming.\n\n" \
                       "Select the shimming algorithm from the dropdown list."
         super().__init__(parent, title, description)
@@ -101,7 +114,7 @@ def unshow_choice_box_sizers(self):
             sizer_item.Show(False)
 
     def create_choice_box(self):
-        self.choice_box = wx.Choice(self, choices=self.dropdown_choices)
+        self.choice_box = wx.Choice(self, choices=self.dropdown_choices, name="b0shim_algorithms")
         self.choice_box.Bind(wx.EVT_CHOICE, self.on_choice)
         self.sizer_run.Add(self.choice_box)
         self.sizer_run.AddSpacer(10)
@@ -114,7 +127,7 @@ def create_sizer_dynamic_shim(self, metadata=None):
             {
                 "button_label": "Number of Custom Coils",
                 "button_function": "add_input_coil_boxes_dyn",
-                "name": "no_arg",
+                "name": "no_arg_ncoils_dyn",
                 "info_text": "Number of phase NIfTI files to be used. Must be an integer > 0.",
             }
         ]
@@ -172,7 +185,6 @@ def create_sizer_dynamic_shim(self, metadata=None):
                 "button_label": "Scanner constraints",
                 "button_function": "select_file",
                 "name": "scanner-coil-constraints",
-                "default_text": f"{os.path.join(__ST_DIR__, 'coil_config.json')}",
             },
         ]
         component_scanner1 = InputComponent(self, input_text_box_metadata_scanner, cli=dynamic_cli)
@@ -288,7 +300,8 @@ def create_sizer_dynamic_shim(self, metadata=None):
                 "name": 'regularization-factor',
             }
         ]
-        component_reg_factor = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
+        component_reg_factor_lsq = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
+        component_reg_factor_qp = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
 
         criteria_dropdown_metadata = [
             {
@@ -318,15 +331,20 @@ def create_sizer_dynamic_shim(self, metadata=None):
                 "label": "Pseudo Inverse",
                 "option_value": "pseudo_inverse"
             },
+            {
+                "label": "Quad Prog",
+                "option_value": "quad_prog"
+            }
         ]
 
         self.dropdown_opt_dyn = DropdownComponent(
             panel=self,
             dropdown_metadata=dropdown_opt_metadata,
             label="Optimizer",
             option_name='optimizer-method',
-            list_components=[dropdown_crit, component_reg_factor, self.create_empty_component()],
-            component_to_dropdown_choice=[0, 0, 1],
+            list_components=[dropdown_crit, component_reg_factor_lsq,
+                             self.create_empty_component(), component_reg_factor_qp],
+            component_to_dropdown_choice=[0, 0, 1, 2],
             cli=dynamic_cli
         )
 
@@ -428,7 +446,7 @@ def create_sizer_dynamic_shim(self, metadata=None):
         dropdown_fatsat1.add_dropdown_parent(self.dropdown_coil_format_dyn)
         dropdown_fatsat2.add_dropdown_parent(self.dropdown_coil_format_dyn)
 
-        run_component = RunComponent(
+        self.run_component_dyn = RunComponent(
             panel=self,
             list_components=[self.component_coils_dyn, component_inputs, self.dropdown_opt_dyn, self.dropdown_slice_dyn,
                              self.dropdown_scanner_order_dyn,
@@ -437,7 +455,7 @@ def create_sizer_dynamic_shim(self, metadata=None):
             output_paths=["fieldmap_calculated_shim_masked.nii.gz",
                           "fieldmap_calculated_shim.nii.gz"]
         )
-        sizer = run_component.sizer
+        sizer = self.run_component_dyn.sizer
         return sizer
 
     def create_sizer_realtime_shim(self, metadata=None):
@@ -448,7 +466,7 @@ def create_sizer_realtime_shim(self, metadata=None):
             {
                 "button_label": "Number of Custom Coils",
                 "button_function": "add_input_coil_boxes_rt",
-                "name": "no_arg",
+                "name": "no_arg_ncoils_rt",
                 "info_text": "Number of phase NIfTI files to be used. Must be an integer > 0.",
             }
         ]
@@ -497,7 +515,6 @@ def create_sizer_realtime_shim(self, metadata=None):
                 "button_label": "Scanner constraints",
                 "button_function": "select_file",
                 "name": "scanner-coil-constraints",
-                "default_text": f"{os.path.join(__ST_DIR__, 'coil_config.json')}",
             },
         ]
         component_scanner1 = InputComponent(self, input_text_box_metadata_scanner, cli=realtime_cli)
@@ -625,7 +642,8 @@ def create_sizer_realtime_shim(self, metadata=None):
                 "name": 'regularization-factor',
             }
         ]
-        component_reg_factor = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
+        component_reg_factor_lsq = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
+        component_reg_factor_qp = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
 
         criteria_dropdown_metadata = [
             {
@@ -655,15 +673,20 @@ def create_sizer_realtime_shim(self, metadata=None):
                 "label": "Pseudo Inverse",
                 "option_value": "pseudo_inverse"
             },
+            {
+                "label": "Quad Prog",
+                "option_value": "quad_prog"
+            }
         ]
 
         self.dropdown_opt_rt = DropdownComponent(
             panel=self,
             dropdown_metadata=dropdown_opt_metadata,
             label="Optimizer",
-            option_name = 'optimizer-method',
-            list_components= [dropdown_crit, component_reg_factor, self.create_empty_component()],
-            component_to_dropdown_choice=[0, 0, 1],
+            option_name='optimizer-method',
+            list_components=[dropdown_crit, component_reg_factor_lsq,
+                             self.create_empty_component(), component_reg_factor_qp],
+            component_to_dropdown_choice=[0, 0, 1, 2],
             cli=realtime_cli
         )
 
@@ -746,7 +769,7 @@ def create_sizer_realtime_shim(self, metadata=None):
 
         dropdown_fatsat.add_dropdown_parent(self.dropdown_coil_format_rt)
 
-        run_component = RunComponent(
+        self.run_component_rt = RunComponent(
             panel=self,
             list_components=[self.component_coils_rt, component_inputs, self.dropdown_opt_rt, self.dropdown_slice_rt,
                              self.dropdown_scanner_order_rt,
@@ -755,7 +778,7 @@ def create_sizer_realtime_shim(self, metadata=None):
             # TODO: output paths
             output_paths=[]
         )
-        sizer = run_component.sizer
+        sizer = self.run_component_rt.sizer
         return sizer
 
     def create_sizer_max_intensity(self, metadata=None):
@@ -781,11 +804,11 @@ def create_sizer_max_intensity(self, metadata=None):
         ]
         component_inputs = InputComponent(self, inputs_metadata, cli=max_intensity_cli)
 
-        run_component = RunComponent(
+        self.run_component_mi = RunComponent(
             panel=self,
             list_components=[component_inputs],
             st_function="st_b0shim max-intensity",
             output_paths=[]
         )
-        sizer = run_component.sizer
+        sizer = self.run_component_mi.sizer
         return sizer

fsleyes_plugin_shimming_toolbox/tabs/b1shim_tab.py

@@ -83,7 +83,7 @@ def unshow_choice_box_sizers(self):
             sizer_item.Show(False)
 
     def create_choice_box(self):
-        self.choice_box = wx.Choice(self, choices=self.dropdown_choices)
+        self.choice_box = wx.Choice(self, choices=self.dropdown_choices, name="b1shim_algorithms")
         self.choice_box.Bind(wx.EVT_CHOICE, self.on_choice)
         self.sizer_run.Add(self.choice_box)
         self.sizer_run.AddSpacer(10)

fsleyes_plugin_shimming_toolbox/tabs/dicom_to_nifti_tab.py

@@ -18,6 +18,7 @@ def __init__(self, parent, title="Dicom to Nifti"):
         super().__init__(parent, title, description)
 
         self.sizer_run = self.create_sizer_run()
+        self.run_component = None
         sizer = self.create_dicom_to_nifti_sizer()
         self.sizer_run.Add(sizer, 0, wx.EXPAND)
 
@@ -52,5 +53,5 @@ def create_dicom_to_nifti_sizer(self):
             }
         ]
         component = InputComponent(self, input_text_box_metadata, cli=dicom_to_nifti_cli)
-        run_component = RunComponent(panel=self, list_components=[component], st_function="st_dicom_to_nifti")
-        return run_component.sizer
+        self.run_component = RunComponent(panel=self, list_components=[component], st_function="st_dicom_to_nifti")
+        return self.run_component.sizer