Uploading example files (sh/yaml)

Author: FabianHoerst

cellvit/utils/ressource_manager.py

@@ -705,7 +705,7 @@ def __init__(self, gpu: int = 0) -> None:
         (cpu_count, memory), env = get_cpu_resources()
         gpu_resources = get_gpu_resources()
 
-        self.cpu_count = cpu_count
+        self.cpu_count = int(cpu_count)
         self.memory = memory
         self.runtime_environment = env
         self.has_gpu = gpu_resources["has_gpu"]
@@ -753,7 +753,7 @@ def overwrite_ray_remote_cpus(self, ray_remote_cpus: int) -> None:
         self.ray_worker = int(available_ray_cpus / self.ray_remote_cpus)
 
     def overwrite_available_cpus(self, cpu_count: int) -> None:
-        self.cpu_count = cpu_count
+        self.cpu_count = int(cpu_count)
         self._calculate_ray_worker()
 
     def overwrite_memory(self, memory: int) -> None:

docs/source/examples.rst

@@ -212,7 +212,7 @@ To see debug messages if errors occur and inspect the tissue detection, you can
             cellvit-inference \
                 --model SAM \
                 --outdir ./test_results/x40_svs/minimal/SAM \
-                --debug
+                --debug \
                 process_wsi \
                 --wsi_path ./test_database/x40_svs/JP2K-33003-2.svs
 
@@ -1077,7 +1077,7 @@ Set the batch-size (amount of 1024 x 1024 patches per batch):
 
             cellvit-inference \
                 --model SAM \
-                --batch_size 32
+                --batch_size 32 \
                 --outdir ./test_results/x40_svs/batch_size/SAM \
                 process_dataset \
                 --wsi_folder ./test_database/x40_svs

examples/cli/basic_hipt.sh

@@ -1,6 +1,5 @@
-python3 ./cellvit/detect_cells.py \
-  --model HIPT \
-  --outdir ./test_results/x40_svs/minimal/HIPT \
-  --cpu_count 16 \
-  process_wsi \
-  --wsi_path ./test_database/x40_svs/JP2K-33003-2.svs
+cellvit-inference \
+    --model HIPT \
+    --outdir ./test_results/x40_svs/minimal/HIPT \
+    process_wsi \
+    --wsi_path ./test_database/x40_svs/JP2K-33003-2.svs

examples/cli/basic_sam.sh

@@ -1,6 +1,5 @@
-python3 ./cellvit/detect_cells.py \
-  --model SAM \
-  --outdir ./test_results/x40_svs/minimal/SAM \
-  --cpu_count 16 \
-  process_wsi \
-  --wsi_path ./test_database/x40_svs/JP2K-33003-2.svs
+cellvit-inference \
+    --model SAM \
+    --outdir ./test_results/x40_svs/minimal/SAM \
+    process_wsi \
+    --wsi_path ./test_database/x40_svs/JP2K-33003-2.svs

examples/cli/basic_sam_binary.sh

@@ -0,0 +1,6 @@
+cellvit-inference \
+    --model SAM \
+    --batch_size 32 \
+    --outdir ./test_results/x40_svs/batch_size/SAM \
+    process_dataset \
+    --wsi_folder ./test_database/x40_svs

examples/cli/basic_sam_geojson.sh

@@ -0,0 +1,6 @@
+cellvit-inference \
+    --model SAM \
+    --nuclei_taxonomy binary \
+    --outdir ./test_results/x40_svs/binary/SAM \
+    process_wsi \
+    --wsi_path ./test_database/x40_svs/JP2K-33003-2.svs

examples/cli/basic_sam_geojson_compression.sh

@@ -0,0 +1,6 @@
+cellvit-inference \
+    --model SAM \
+    --outdir ./test_results/x40_svs/cpu_count/SAM \
+    --cpu_count 16 \
+    process_dataset \
+    --wsi_folder ./test_database/x40_svs