Add 3rd order support (#68)

* FSLeyes is not updated to support numpy 2.0

* Add support for 3rd order, fix bug with scanner orders for rt shimming, add test for rt

* Switch to indicate python 3.10

.github/workflows/tests.yml

@@ -24,7 +24,7 @@ jobs:
           - 'ubuntu-22.04'
           - 'ubuntu-20.04'
         python-version:
-          - '3.9'
+          - '3.10'
 
     steps:
       - name: Get home directory

fsleyes_plugin_shimming_toolbox/components/run_component.py

@@ -185,21 +185,21 @@ def get_run_args(self, st_function):
         msg = "Running "
         # Split is necessary if we have grouped commands (st_mask threshold)
         command = st_function.split(' ')
-    
-        for component in self.list_components:  
-            
+
+        for component in self.list_components:
+
             cmd, output, load_in_overlay = component.get_command()
             command.extend(cmd)
-            
-            if st_function.split(' ')[-1] == "realtime-dynamic" and cmd[0] == "--coil":
+
+            if st_function.split(' ')[-1] == "realtime-dynamic" and cmd and cmd[0] == "--coil":
                 cmd_riro = ['--coil-riro' if i == '--coil' else i for i in cmd]
                 command.extend(cmd_riro)
-                
+
             self.load_in_overlay.extend(load_in_overlay)
-            
+
             if output:
                 self.output = output
-                
+
         msg += ' '.join(command) + '\n'
 
         return command, msg

fsleyes_plugin_shimming_toolbox/tabs/b0shim_tab.py

@@ -233,6 +233,10 @@ def create_sizer_dynamic_shim(self, metadata=None):
             {
                 "label": "2",
                 "option_value": "2"
+            },
+            {
+                "label": "3",
+                "option_value": "3"
             }
         ]
 
@@ -241,8 +245,8 @@ def create_sizer_dynamic_shim(self, metadata=None):
             label="Scanner Order",
             checkbox_metadata=checkbox_scanner_order_metadata,
             option_name='scanner-coil-order',
-            components_dict=[{'object': dropdown_scanner_format, 'checkbox': ['f0', '1', '2']},
-                             {'object': component_scanner, 'checkbox': ['f0', '1', '2']}],
+            components_dict=[{'object': dropdown_scanner_format, 'checkbox': ['f0', '1', '2', '3']},
+                             {'object': component_scanner, 'checkbox': ['f0', '1', '2', '3']}],
         )
 
         dropdown_ovf_metadata = [
@@ -283,6 +287,10 @@ def create_sizer_dynamic_shim(self, metadata=None):
                 "label": "Mean Absolute Error",
                 "option_value": "mae",
             },
+            {
+                "label": "Root Mean Squared Error",
+                "option_value": "rmse",
+            }
         ]
 
         dropdown_crit = DropdownComponent(
@@ -520,7 +528,7 @@ def create_sizer_realtime_shim(self, metadata=None):
             panel=self,
             dropdown_metadata=dropdown_scanner_format_metadata,
             label="Scanner Output Format",
-            option_name = 'output-file-format-scanner',
+            option_name='output-file-format-scanner',
             cli=realtime_cli
         )
 
@@ -531,12 +539,17 @@ def create_sizer_realtime_shim(self, metadata=None):
             },
             {
                 "label": "1",
-                "option_value": "0,1"
+                "option_value": "1"
             },
             {
                 "label": "2",
-                "option_value": "0,1,2"
-            }
+                "option_value": "2"
+            },
+            {
+                "label": "3",
+                "option_value": "3"
+            },
+
         ]
 
         input_text_box_metadata_scanner = [
@@ -547,14 +560,14 @@ def create_sizer_realtime_shim(self, metadata=None):
             },
         ]
         component_scanner = InputComponent(self, input_text_box_metadata_scanner, cli=realtime_cli)
-            
+
         self.checkbox_scanner_order_rt = CheckboxComponent(
             panel=self,
             label="Scanner Order",
             checkbox_metadata=checkbox_scanner_order_metadata,
             option_name='scanner-coil-order',
-            components_dict=[{'object': dropdown_scanner_format, 'checkbox': ['f0', '1', '2']},
-                             {'object': component_scanner, 'checkbox': ['f0', '1', '2']}],
+            components_dict=[{'object': dropdown_scanner_format, 'checkbox': ['f0', '1', '2', '3']},
+                             {'object': component_scanner, 'checkbox': ['f0', '1', '2', '3']}],
             additional_sizer_dict={'info text': None, 'label': 'Scanner Order RIRO',
                                    'option name': 'scanner-coil-order-riro',
                                    'checkbox metadata': checkbox_scanner_order_metadata}
@@ -575,7 +588,7 @@ def create_sizer_realtime_shim(self, metadata=None):
             panel=self,
             dropdown_metadata=dropdown_ovf_metadata,
             label="Output Value Format",
-            option_name = 'output-value-format',
+            option_name='output-value-format',
             cli=realtime_cli
         )
 
@@ -598,6 +611,10 @@ def create_sizer_realtime_shim(self, metadata=None):
                 "label": "Mean Absolute Error",
                 "option_value": "mae",
             },
+            {
+                "label": "Root Mean Squared Error",
+                "option_value": "rmse",
+            }
         ]
 
         dropdown_crit = DropdownComponent(
@@ -659,7 +676,7 @@ def create_sizer_realtime_shim(self, metadata=None):
             panel=self,
             dropdown_metadata=dropdown_slice_metadata,
             label="Slice Ordering",
-            option_name = 'slices',
+            option_name='slices',
             list_components=[self.create_empty_component(),
                              component_slice_seq,
                              component_slice_int,
@@ -686,7 +703,7 @@ def create_sizer_realtime_shim(self, metadata=None):
             panel=self,
             dropdown_metadata=dropdown_fatsat_metadata,
             label="Fat Saturation",
-            option_name = 'fatsat',
+            option_name='fatsat',
             cli=realtime_cli
         )
 
@@ -705,7 +722,7 @@ def create_sizer_realtime_shim(self, metadata=None):
             panel=self,
             dropdown_metadata=dropdown_coil_format_metadata,
             label="Custom Coil Output Format",
-            option_name = 'output-file-format-coil',
+            option_name='output-file-format-coil',
             cli=realtime_cli,
             list_components=[self.create_empty_component(),
                              dropdown_fatsat]

installer/install_shimming_toolbox.sh

@@ -14,7 +14,7 @@ rm -rf "${ST_DIR}/shimming-toolbox"
 
 print info "Downloading Shimming-Toolbox"
 
-ST_VERSION="7701d3ae54f1335c101b7d197b002a46a2e569d2"
+ST_VERSION="cf28d353240fd510de1e8aa492c6c23ae57e66bd"
 
 curl -L "https://github.com/shimming-toolbox/shimming-toolbox/archive/${ST_VERSION}.zip" > "shimming-toolbox-${ST_VERSION}.zip"
 

setup.py

@@ -4,7 +4,8 @@
     name='fsleyes-plugin-shimming-toolbox',
     install_requires=[
         "imageio",
-        'pre-commit>=2.10.0'
+        'pre-commit>=2.10.0',
+        'numpy<2.0'
     ],
     packages=find_packages(exclude=['.git']),
     include_package_data=True,