Add multiple fieldmap and b0shim tests

fsleyes_plugin_shimming_toolbox/tabs/fieldmap_tab.py

@@ -16,6 +16,8 @@
 class FieldMapTab(Tab):
     def __init__(self, parent, title="Fieldmap"):
 
+        self.component_save_mask1 = None
+        self.component_save_mask2 = None
         self.run_component = None
         self.component_input2 = None
         self.component_output = None
@@ -84,16 +86,30 @@ def create_fieldmap_sizer(self):
             input_text_box_metadata=mask_metadata,
             cli=prepare_fieldmap_cli
         )
+        save_mask_metadata = [
+            {
+                "button_label": "Output Calculated Mask",
+                "name": "savemask",
+                "load_in_overlay": True
+            }
+        ]
+
+        self.component_save_mask1 = InputComponent(
+            panel=self,
+            input_text_box_metadata=save_mask_metadata,
+            cli=prepare_fieldmap_cli
+        )
+
+        self.component_save_mask2 = InputComponent(
+            panel=self,
+            input_text_box_metadata=save_mask_metadata,
+            cli=prepare_fieldmap_cli
+        )
 
         threshold_metadata = [
             {
                 "button_label": "Threshold",
                 "name": "threshold",
-            },
-            {
-                "button_label": "Output Calculated Mask",
-                "name": "savemask",
-                "load_in_overlay": True
             }
         ]
         self.component_threshold = InputComponent(
@@ -123,7 +139,8 @@ def create_fieldmap_sizer(self):
             label="Unwrapping region",
             info_text="Masking methods either with a file input or a threshold",
             option_name='no_arg_roi',
-            list_components=[self.create_empty_component(), self.component_mask, self.component_threshold],
+            list_components=[self.component_save_mask1, self.component_mask, self.component_threshold, self.component_save_mask2],
+            component_to_dropdown_choice=[0, 1, 2, 2],
             cli=prepare_fieldmap_cli
         )
 

test/gui/test_b0shim_tab.py

@@ -17,11 +17,67 @@
 from fsleyes_plugin_shimming_toolbox.tabs.b0shim_tab import B0ShimTab
 
 
-def test_st_plugin_b0shim_run():
-    run_with_orthopanel(_test_st_plugin_b0shim_run)
-
-
-def _test_st_plugin_b0shim_run(view, overlayList, displayCtx):
+def test_st_plugin_b0shim_dyn_lsq_mse():
+    options = {'optimizer-method': 'Least Squares',
+               'optimizer-criteria': 'Mean Squared Error',
+               'slices': 'Auto detect',
+               'scanner-coil-order': '1',
+               'output-file-format-scanner': 'Slicewise per Channel',
+               'output-file-format-coil': 'Slicewise per Channel',
+               'fatsat': 'Auto detect',
+               'output-value-format': 'delta'
+               }
+
+    def _test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options)
+    run_with_orthopanel(_test_st_plugin_b0shim_dyn)
+
+
+def test_st_plugin_b0shim_dyn_lsq_mae():
+    options = {'optimizer-method': 'Least Squares',
+               'optimizer-criteria': 'Mean Absolute Error',
+               'slices': 'Auto detect',
+               'scanner-coil-order': '1',
+               'output-file-format-scanner': 'Slicewise per Channel',
+               'output-file-format-coil': 'Slicewise per Channel',
+               'output-value-format': 'delta'
+               }
+
+    def _test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options)
+    run_with_orthopanel(_test_st_plugin_b0shim_dyn)
+
+
+def test_st_plugin_b0shim_dyn_pi():
+    options = {'optimizer-method': 'Pseudo Inverse',
+               'slices': 'Auto detect',
+               'scanner-coil-order': '1',
+               'output-file-format-scanner': 'Slicewise per Channel',
+               'output-file-format-coil': 'Slicewise per Channel',
+               'output-value-format': 'delta'
+               }
+
+    def _test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options)
+    run_with_orthopanel(_test_st_plugin_b0shim_dyn)
+
+
+def test_st_plugin_b0shim_dyn_qp():
+    options = {'optimizer-method': 'Quad Prog',
+               'optimizer-criteria': 'Mean Squared Error',
+               'slices': 'Auto detect',
+               'scanner-coil-order': '1',
+               'output-file-format-scanner': 'Slicewise per Channel',
+               'output-file-format-coil': 'Slicewise per Channel',
+               'output-value-format': 'delta'
+               }
+
+    def _test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options)
+    run_with_orthopanel(_test_st_plugin_b0shim_dyn)
+
+
+def __test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options):
     """ Makes sure the B0 shim tab runs (Add dummy input and simulate a click) """
     nb_terminal = get_notebook(view)
 
@@ -61,17 +117,39 @@ def _test_st_plugin_b0shim_run(view, overlayList, displayCtx):
         for widget in list_widgets:
             if isinstance(widget, wx.Choice) and widget.IsShown():
                 if widget.GetName() == 'optimizer-method':
-                    assert set_dropdown_selection(widget, 'Least Squares')
+                    assert set_dropdown_selection(widget, options['optimizer-method'])
+                if widget.GetName() == 'scanner-coil-order':
+                    assert set_dropdown_selection(widget, options['scanner-coil-order'])
+                if widget.GetName() == 'slices':
+                    assert set_dropdown_selection(widget, options['slices'])
                 if widget.GetName() == 'scanner-coil-order':
-                    assert set_dropdown_selection(widget, '1')
-                # optimizer-criteria, slices, scanner-coil-order, output-file-format-scanner, output-file-format-coil,
-                # fatsat, output-value-format
+                    assert set_dropdown_selection(widget, options['scanner-coil-order'])
+                if widget.GetName() == 'output-value-format':
+                    assert set_dropdown_selection(widget, options['output-value-format'])
+        # Select the dropdowns that are nested
+        list_widgets = []
+        get_all_children(b0shim_tab.sizer_run, list_widgets)
+        for widget in list_widgets:
+            if isinstance(widget, wx.Choice) and widget.IsShown():
+                if widget.GetName() == 'optimizer-criteria':
+                    assert set_dropdown_selection(widget, options['optimizer-criteria'])
+                if widget.GetName() == 'output-file-format-scanner':
+                    assert set_dropdown_selection(widget, options['output-file-format-scanner'])
+                if widget.GetName() == 'output-file-format-scanner':
+                    assert set_dropdown_selection(widget, options['output-file-format-coil'])
+        # Select the dropdowns that are nested
+        list_widgets = []
+        get_all_children(b0shim_tab.sizer_run, list_widgets)
+        for widget in list_widgets:
+            if isinstance(widget, wx.Choice) and widget.IsShown():
+                if widget.GetName() == 'fatsat':
+                    assert set_dropdown_selection(widget, options['fatsat'])
 
         # Fill in the text boxes
         list_widgets = []
         get_all_children(b0shim_tab.sizer_run, list_widgets)
         for widget in list_widgets:
-            if isinstance(widget, wx.TextCtrl):
+            if isinstance(widget, wx.TextCtrl) and widget.IsShown():
                 if widget.GetName() == 'no_arg_ncoils_dyn':
                     widget.SetValue('0')
                     realYield()

test/gui/test_dicom_to_nifti_tab.py

@@ -35,7 +35,7 @@ def _test_st_plugin_dcm2niix_run(view, overlayList, displayCtx):
         list_widgets = []
         get_all_children(dcm2nifti_tab.sizer_run, list_widgets)
         for widget in list_widgets:
-            if isinstance(widget, wx.TextCtrl):
+            if isinstance(widget, wx.TextCtrl) and widget.IsShown():
                 if widget.GetName() == 'input':
                     widget.SetValue(path_input)
                     realYield()

test/gui/test_fieldmap_tab.py

@@ -1,23 +1,62 @@
 #!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
+import nibabel as nib
+import numpy as np
 import os
 import pathlib
+from shimmingtoolbox.masking.shapes import shapes
 import tempfile
 import time
 import wx
 
-from .test_tabs import get_notebook, set_notebook_page, get_tab, get_all_children
+from .test_tabs import get_notebook, set_notebook_page, get_tab, get_all_children, set_dropdown_selection
 from .. import realYield, run_with_orthopanel
 from fsleyes_plugin_shimming_toolbox import __dir_testing__
 from fsleyes_plugin_shimming_toolbox.tabs.fieldmap_tab import FieldMapTab
 
 
-def test_st_plugin_fieldmap_run():
-    run_with_orthopanel(_test_st_plugin_fieldmap_run)
+def test_st_plugin_fieldmap_prelude():
+    options = {'no_arg_roi': 'auto threshold',
+               'unwrapper': 'Prelude'}
 
+    def _test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options)
 
-def _test_st_plugin_fieldmap_run(view, overlayList, displayCtx):
+    run_with_orthopanel(_test_st_plugin_fieldmap)
+
+
+def test_st_plugin_fieldmap_skimage():
+    options = {'no_arg_roi': 'auto threshold',
+               'unwrapper': 'Skimage'}
+
+    def _test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options)
+
+    run_with_orthopanel(_test_st_plugin_fieldmap)
+
+
+def test_st_plugin_fieldmap_input_mask():
+    options = {'no_arg_roi': 'mask',
+               'unwrapper': 'Skimage'}
+
+    def _test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options)
+
+    run_with_orthopanel(_test_st_plugin_fieldmap)
+
+
+def test_st_plugin_fieldmap_threshold():
+    options = {'no_arg_roi': 'threshold',
+               'unwrapper': 'Skimage'}
+
+    def _test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options):
+        __test_st_plugin_fieldmap(view, overlayList, displayCtx, options=options)
+
+    run_with_orthopanel(_test_st_plugin_fieldmap)
+
+
+def __test_st_plugin_fieldmap(view, overlayList, displayCtx, options):
     """ Makes sure fieldmap tab can be run (Add dummy input and simulate a click) """
     nb_terminal = get_notebook(view)
 
@@ -33,6 +72,8 @@ def _test_st_plugin_fieldmap_run(view, overlayList, displayCtx):
         fname_phase1 = os.path.join(__dir_testing__, 'ds_b0', 'sub-fieldmap', 'fmap', 'sub-fieldmap_phase1.nii.gz')
         fname_phase2 = os.path.join(__dir_testing__, 'ds_b0', 'sub-fieldmap', 'fmap', 'sub-fieldmap_phase2.nii.gz')
         fname_output = os.path.join(tmp, 'fieldmap.nii.gz')
+        fname_input_mask = os.path.join(tmp, 'input_mask.nii.gz')
+        fname_output_mask = os.path.join(tmp, 'output_mask.nii.gz')
 
         # Fill in Fieldmap tab options
         list_widgets = []
@@ -45,7 +86,17 @@ def _test_st_plugin_fieldmap_run(view, overlayList, displayCtx):
         list_widgets = []
         get_all_children(fmap_tab.sizer_run, list_widgets)
         for widget in list_widgets:
-            if isinstance(widget, wx.TextCtrl):
+            if isinstance(widget, wx.Choice) and widget.IsShown():
+                if widget.GetName() == 'no_arg_roi':
+                    assert set_dropdown_selection(widget, options['no_arg_roi'])
+                    # auto threshold, mask, threshold
+                if widget.GetName() == 'unwrapper':
+                    assert set_dropdown_selection(widget, options['unwrapper'])
+                    # Prelude, Skimage
+        list_widgets = []
+        get_all_children(fmap_tab.sizer_run, list_widgets)
+        for widget in list_widgets:
+            if isinstance(widget, wx.TextCtrl) and widget.IsShown():
                 if widget.GetName() == 'input_phase_1':
                     widget.SetValue(fname_phase1)
                     realYield()
@@ -61,6 +112,14 @@ def _test_st_plugin_fieldmap_run(view, overlayList, displayCtx):
                 if widget.GetName() == 'output':
                     widget.SetValue(fname_output)
                     realYield()
+                if widget.GetName() == 'mask':
+                    nii_mask = get_mask_from_fmap()
+                    nib.save(nii_mask, fname_input_mask)
+                    widget.SetValue(fname_input_mask)
+                    realYield()
+                if widget.GetName() == 'savemask':
+                    widget.SetValue(fname_output_mask)
+                    realYield()
 
         # Call the function ran when clicking run button
         fmap_tab.run_component.run()
@@ -77,3 +136,25 @@ def _test_st_plugin_fieldmap_run(view, overlayList, displayCtx):
         # Make sure there is an output in the overlay (that would mean the ST CLI ran)
         assert overlay_file is not None
         assert os.path.exists(fname_output)
+        if options['no_arg_roi'] == 'mask':
+            assert not os.path.exists(fname_output_mask)
+        elif options['no_arg_roi'] == 'threshold':
+            assert os.path.exists(fname_output_mask)
+        else:
+            # auto threshold
+            assert os.path.exists(fname_output_mask)
+
+
+
+def get_mask_from_fmap():
+    fname_mag = os.path.join(__dir_testing__, 'ds_b0', 'sub-fieldmap', 'fmap', 'sub-fieldmap_magnitude1.nii.gz')
+    nii_fmap = nib.load(fname_mag)
+    nx, ny, nz = nii_fmap.shape
+
+    mask = shapes(nii_fmap.get_fdata(), 'cube',
+                  center_dim1=int(nx / 2),
+                  center_dim2=int(ny / 2),
+                  len_dim1=10, len_dim2=10, len_dim3=nz - 10)
+
+    nii_mask = nib.Nifti1Image(mask.astype(np.uint8), nii_fmap.affine)
+    return nii_mask