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catalystneuro · Nov 22, 2024 · 7222448 · 7222448
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commit 7222448
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Showing 4 changed files with 28 additions and 37 deletions.
diff --git a/examples/example_1.py b/examples/example_1.py
@@ -9,7 +9,7 @@
 )
 
 
-service_name = os.getenv('DENDRO_SERVICE_NAME', 'luiz-dandihub-service')
+service_name = os.getenv("DENDRO_SERVICE_NAME", "luiz-dandihub-service")
 
 
 # Using this file: https://dandiarchive.org/dandiset/000350/0.240822.1759/files?location=sub-20161022-1&page=1
@@ -21,41 +21,32 @@ def main():
         "timepoints": 1000,
     }
     job_def = DendroJobDefinition(
-        appName='voluseg',
-        processorName='voluseg_processor',
+        appName="voluseg",
+        processorName="voluseg_processor",
         inputFiles=[
             DendroJobInputFile(
-                name='input',
-                fileBaseName='sub-20161022-1',
+                name="input",
+                fileBaseName="sub-20161022-1",
                 url="https://dandiarchive.s3.amazonaws.com/blobs/057/ecb/057ecbef-e732-4e94-8d99-40ebb74d346e",
             )
         ],
-        outputFiles=[
-            DendroJobOutputFile(
-                name='output',
-                fileBaseName='output.txt'
-            )
-        ],
+        outputFiles=[DendroJobOutputFile(name="output", fileBaseName="output.txt")],
         parameters=[
-            DendroJobParameter(name=k, value=v)
-            for k, v in parameters_dict.items()
-        ]
+            DendroJobParameter(name=k, value=v) for k, v in parameters_dict.items()
+        ],
     )
     required_resources = DendroJobRequiredResources(
-        numCpus=24,
-        numGpus=0,
-        memoryGb=120,
-        timeSec=6*3600
+        numCpus=24, numGpus=0, memoryGb=120, timeSec=6 * 3600
     )
     job = submit_job(
         service_name=service_name,
         job_definition=job_def,
         required_resources=required_resources,
         target_compute_client_ids=["*"],
-        tags=['example'],
+        tags=["example"],
     )
     print(job.job_url, job.status)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/voluseg/VolusegProcessor.py b/voluseg/VolusegProcessor.py
@@ -3,16 +3,17 @@
 
 
 class VolusegProcessor(ProcessorBase):
-    name = 'voluseg_processor'
-    description = 'Run Voluseg for volumetric segmentation.'
-    label = 'voluseg_processor'
-    image = 'ghcr.io/catalystneuro/dendro-voluseg:latest'
-    executable = '/app/main.py'
+    name = "voluseg_processor"
+    description = "Run Voluseg for volumetric segmentation."
+    label = "voluseg_processor"
+    image = "ghcr.io/catalystneuro/dendro-voluseg:latest"
+    executable = "/app/main.py"
     attributes = {}
 
     @staticmethod
     def run(context: VolusegContext):
         import os
+
         # import lindi
         import voluseg
 

diff --git a/voluseg/context.py b/voluseg/context.py
@@ -2,17 +2,19 @@
 
 
 class VolusegContext(BaseModel):
-    input: InputFile = Field(description='Input NWB file in .nwb or .nwb.lindi.tar format')
-    output: OutputFile = Field(description='Output embedding in .lindi.tar format')
+    input: InputFile = Field(
+        description="Input NWB file in .nwb or .nwb.lindi.tar format"
+    )
+    output: OutputFile = Field(description="Output embedding in .lindi.tar format")
     detrending: str = Field(
         default="standard",
         description="Type of detrending: 'standard', 'robust', or 'none'",
-        json_schema_extra={'options': ["standard", "robust", "none"]},
+        json_schema_extra={"options": ["standard", "robust", "none"]},
     )
     registration: str = Field(
         default="medium",
         description="Quality of registration: 'high', 'medium', 'low' or 'none'",
-        json_schema_extra={'options': ["high", "medium", "low", "none"]},
+        json_schema_extra={"options": ["high", "medium", "low", "none"]},
     )
     registration_restrict: str = Field(
         default="",
@@ -49,12 +51,12 @@ class VolusegContext(BaseModel):
     type_timepoints: str = Field(
         default="dff",
         description="Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom'",
-        json_schema_extra={'options': ["dff", "periodic", "custom"]},
+        json_schema_extra={"options": ["dff", "periodic", "custom"]},
     )
     type_mask: str = Field(
         default="geomean",
         description="Type of volume averaging for mask: 'mean', 'geomean' or 'max'",
-        json_schema_extra={'options': ["mean", "geomean", "max"]},
+        json_schema_extra={"options": ["mean", "geomean", "max"]},
     )
     timepoints: int = Field(
         default=1000,

diff --git a/voluseg/main.py b/voluseg/main.py
@@ -2,13 +2,10 @@
 from VolusegProcessor import VolusegProcessor
 
 
-app = App(
-    app_name='voluseg',
-    description='Voluseg processors'
-)
+app = App(app_name="voluseg", description="Voluseg processors")
 
 app.add_processor(VolusegProcessor)
 
 
-if __name__ == '__main__':
-    app.run()
+if __name__ == "__main__":
+    app.run()