Ab/signal recovery (#70)

* Add grad optimizer and change sequential ordering * Add test for signal loss optimization * Change to updated commmit on ST
shimming-toolbox · Jun 27, 2024 · 6d1d777 · 6d1d777
1 parent c580658
commit 6d1d777
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Showing 3 changed files with 55 additions and 9 deletions.
diff --git a/fsleyes_plugin_shimming_toolbox/tabs/b0shim_tab.py b/fsleyes_plugin_shimming_toolbox/tabs/b0shim_tab.py
@@ -169,7 +169,8 @@ def create_sizer_dynamic_shim(self, metadata=None):
             },
         ]
         component_slice_int = InputComponent(self, input_text_box_metadata_slice, cli=dynamic_cli)
-        component_slice_seq = InputComponent(self, input_text_box_metadata_slice, cli=dynamic_cli)
+        component_slice_asc = InputComponent(self, input_text_box_metadata_slice, cli=dynamic_cli)
+        component_slice_des = InputComponent(self, input_text_box_metadata_slice, cli=dynamic_cli)
 
         output_metadata = [
             {
@@ -277,7 +278,16 @@ def create_sizer_dynamic_shim(self, metadata=None):
         ]
         component_reg_factor_lsq = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
         component_reg_factor_qp = InputComponent(self, reg_factor_metadata, cli=dynamic_cli)
-
+
+        weighting_signal_loss_metadata = [
+            {
+                "button_label": "Weighting signal loss",
+                "name": "weighting-signal-loss",
+                "default_text": "0.01",
+            },
+        ]
+        component_slice_w_sig_loss = InputComponent(self, weighting_signal_loss_metadata, cli=dynamic_cli)
+
         criteria_dropdown_metadata = [
             {
                 "label": "Mean Squared Error",
@@ -290,15 +300,23 @@ def create_sizer_dynamic_shim(self, metadata=None):
             {
                 "label": "Root Mean Squared Error",
                 "option_value": "rmse",
+            },
+            {
+                "label": "Mean Squared Error + Z gradient",
+                "option_value": "grad",
             }
-        ]
+        ]        
 
         dropdown_crit = DropdownComponent(
             panel=self,
             dropdown_metadata=criteria_dropdown_metadata,
             label="Optimizer Criteria",
             option_name='optimizer-criteria',
-            cli=dynamic_cli
+            cli=dynamic_cli,
+            list_components=[self.create_empty_component(),
+                            self.create_empty_component(),
+                            self.create_empty_component(),
+                            component_slice_w_sig_loss]
         )
 
         dropdown_opt_metadata = [
@@ -335,8 +353,12 @@ def create_sizer_dynamic_shim(self, metadata=None):
                 "option_value": "auto"
             },
             {
-                "label": "Sequential",
-                "option_value": "sequential"
+                "label": "Ascending",
+                "option_value": "ascending"
+            },
+            {
+                "label": "Descending",
+                "option_value": "descending"
             },
             {
                 "label": "Interleaved",
@@ -345,7 +367,7 @@ def create_sizer_dynamic_shim(self, metadata=None):
             {
                 "label": "Volume",
                 "option_value": "volume"
-            },
+            }
         ]
 
         self.dropdown_slice_dyn = DropdownComponent(
@@ -355,7 +377,8 @@ def create_sizer_dynamic_shim(self, metadata=None):
             cli=dynamic_cli,
             option_name='slices',
             list_components=[self.create_empty_component(),
-                             component_slice_seq,
+                             component_slice_asc,
+                             component_slice_des,
                              component_slice_int,
                              self.create_empty_component()]
         )

diff --git a/installer/install_shimming_toolbox.sh b/installer/install_shimming_toolbox.sh
@@ -14,7 +14,7 @@ rm -rf "${ST_DIR}/shimming-toolbox"
 
 print info "Downloading Shimming-Toolbox"
 
-ST_VERSION="cf28d353240fd510de1e8aa492c6c23ae57e66bd"
+ST_VERSION="cb579afefb8ac742909e5d706a85c2c6dc091274"
 
 curl -L "https://github.com/shimming-toolbox/shimming-toolbox/archive/${ST_VERSION}.zip" > "shimming-toolbox-${ST_VERSION}.zip"
 

diff --git a/test/gui/test_b0shim_tab.py b/test/gui/test_b0shim_tab.py
@@ -35,6 +35,22 @@ def _test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options=options):
 
 
 def test_st_plugin_b0shim_dyn_lsq_mae():
+    options = {'optimizer-method': 'Least Squares',
+               'optimizer-criteria': 'Mean Squared Error + Z gradient',
+               'weighting-signal-loss': '0.01',
+               '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_lsq_grad():
     options = {'optimizer-method': 'Least Squares',
                'optimizer-criteria': 'Mean Absolute Error',
                'slices': 'Auto detect',
@@ -106,6 +122,13 @@ def __test_st_plugin_b0shim_dyn(view, overlayList, displayCtx, options):
 
     with tempfile.TemporaryDirectory(prefix='st_' + pathlib.Path(__file__).stem) as tmp:
         nii_fmap, nii_anat, nii_mask, nii_coil, fm_data, anat_data, coil_data, _ = _define_inputs(fmap_dim=3)
+
+        # Duplicate nii_fmap's last dimension
+        if 'weighting-signal-loss' in options.keys():
+            fmap = nii_fmap.get_fdata()
+            fmap = np.repeat(fmap, 5, axis=2)
+            nii_fmap = nib.Nifti1Image(fmap, nii_fmap.affine, header=nii_fmap.header)
+
         fname_fmap = os.path.join(tmp, 'fmap.nii.gz')
         fname_fm_json = os.path.join(tmp, 'fmap.json')
         fname_mask = os.path.join(tmp, 'mask.nii.gz')