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Add 3rd order support #68

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merged 3 commits into from
Jun 18, 2024
Merged

Add 3rd order support #68

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6d12edc
FSLeyes is not updated to support numpy 2.0
po09i Jun 17, 2024
269983f
Add support for 3rd order, fix bug with scanner orders for rt shimmin…
po09i Jun 17, 2024
3e7c376
Switch to indicate python 3.10
po09i Jun 17, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ jobs:
- 'ubuntu-22.04'
- 'ubuntu-20.04'
python-version:
- '3.9'
- '3.10'

steps:
- name: Get home directory
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16 changes: 8 additions & 8 deletions fsleyes_plugin_shimming_toolbox/components/run_component.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
43 changes: 30 additions & 13 deletions fsleyes_plugin_shimming_toolbox/tabs/b0shim_tab.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,10 @@ def create_sizer_dynamic_shim(self, metadata=None):
{
"label": "2",
"option_value": "2"
},
{
"label": "3",
"option_value": "3"
}
]

Expand All @@ -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 = [
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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
)

Expand All @@ -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 = [
Expand All @@ -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}
Expand All @@ -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
)

Expand All @@ -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(
Expand Down Expand Up @@ -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,
Expand All @@ -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
)

Expand All @@ -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]
Expand Down
2 changes: 1 addition & 1 deletion installer/install_shimming_toolbox.sh
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Expand Up @@ -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"

Expand Down
3 changes: 2 additions & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
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