【Fix】 fix cell_segment

STOmics · Dec 4, 2023 · f69952f · f69952f
1 parent 91c0ec1
commit f69952f
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Showing 3 changed files with 22 additions and 21 deletions.
diff --git a/docs/source/Tutorials/Cell_Segmentation.ipynb b/docs/source/Tutorials/Cell_Segmentation.ipynb
@@ -29,9 +29,9 @@
     "\n",
     "Install necessary packages by running commands as below:\n",
     "\n",
-    "> &ensp;&ensp; **pip install tensorflow==2.7.0**  \n",
-    "> &ensp;&ensp; **pip install torch==1.10.0**  \n",
-    "> &ensp;&ensp; **pip install torchvision==0.11.1**  \n",
+    "> &ensp;&ensp; **pip install tensorflow==2.7.0**\n",
+    "> &ensp;&ensp; **pip install torch==1.10.0**\n",
+    "> &ensp;&ensp; **pip install torchvision==0.11.1**\n",
     "> &ensp;&ensp; **pip install albumentations==0.4.6**\n",
     "\n",
     "</div>"
@@ -136,14 +136,15 @@
     "model = './cell_segmetation_v3.0.onnx'\n",
     "image = './SS200000135TL_D1_regist.tif'\n",
     "output = './result_v3'\n",
-    "tissue_seg_model = \"/data/users/wenzhenbin/script/cell_seg/weight_tissue_cut_tool_220304.hdf5\"\n",
+    "tissue_seg_model = \"./weight_tissue_cut_tool_220304.hdf5\"\n",
     "\n",
     "im.cell_seg_v3(\n",
     "    model_path=model,\n",
     "    img_path=image,\n",
     "    out_path=output,\n",
     "    need_tissue_cut=True,\n",
     "    gpu=0,\n",
+    "    is_water=False,\n",
     "    tissue_seg_model_path=tissue_seg_model,\n",
     "    tissue_seg_method=1\n",
     "    )"
@@ -180,10 +181,10 @@
    "source": [
     "from stereo import image as im\n",
     "\n",
-    "model = './cell_segmetation_v3.0.onnx'\n",
+    "model = './cellseg_bcdu_SHDI_221008_tf.onnx'\n",
     "image = './SS200000135TL_D1_regist.tif'\n",
     "output = './result_v3_new'\n",
-    "tissue_seg_model = \"//weight_tissue_cut_tool_220304.hdf5\"\n",
+    "tissue_seg_model = \"/weight_tissue_cut_tool_220304.hdf5\"\n",
     "\n",
     "im.cell_seg(\n",
     "    model_path=model,\n",
@@ -193,7 +194,7 @@
     "    gpu=0,\n",
     "    tissue_seg_model_path=tissue_seg_model,\n",
     "    tissue_seg_method=1,\n",
-    "    version='v3'\n",
+    "    method='v3'\n",
     "    )"
    ]
   },
@@ -442,8 +443,8 @@
     "    out_path=output,\n",
     "    tissue_seg_model_path=tissue_seg_model,\n",
     "    tissue_seg_method=1,\n",
-    "    num_threads=60\n",
-    "    version=\"v1\"\n",
+    "    num_threads=60,\n",
+    "    method=\"v1\"\n",
     "    )"
    ]
   },
@@ -2334,7 +2335,7 @@
    "source": [
     "from stereo import image as im\n",
     "\n",
-    "model = './cell_segmentation_v1.0_pro.onnx'\n",
+    "model = './best_model.pth'\n",
     "image = './SS200000135TL_D1_regist.tif'\n",
     "output = './result_v1_pro'\n",
     "tissue_seg_model = \"./weight_tissue_cut_tool_220304.hdf5\"\n",
@@ -2345,8 +2346,9 @@
     "    out_path=output,\n",
     "    tissue_seg_model_path=tissue_seg_model,\n",
     "    tissue_seg_method=1,\n",
-    "    gpu=0, \n",
-    "    version=\"v1_pro\"\n",
+    "    gpu=0,\n",
+    "    deep_crop_size=256,\n",
+    "    method=\"v1_pro\"\n",
     "    )"
    ]
   },
@@ -2418,15 +2420,17 @@
     }
    ],
    "source": [
-    "model = './cell_segmentation_deepcell/'\n",
+    "from stereo import image as im\n",
+    "\n",
     "image = './SS200000135TL_D1_regist.tif'\n",
     "output = './deepcell/'\n",
+    "model_path ='./'\n",
     "tissue_seg_model = \"./weight_tissue_cut_tool_220304.hdf5\"\n",
     "\n",
     "im.cell_seg_deepcell(\n",
-    "    model_dir=model,\n",
     "    img_path=image,\n",
     "    out_path=output,\n",
+    "    model_path = model_path,\n",
     "    tissue_seg_model_path=tissue_seg_model,\n",
     "    tissue_seg_method=1\n",
     "    )"
@@ -2494,9 +2498,9 @@
     "\n",
     "Install necessary packages by running commands as below:\n",
     "\n",
-    "> &ensp;&ensp; **pip install patchify**  \n",
-    "> &ensp;&ensp; **pip install torch**  \n",
-    "> &ensp;&ensp; **pip install fastremap**  \n",
+    "> &ensp;&ensp; **pip install patchify**\n",
+    "> &ensp;&ensp; **pip install torch**\n",
+    "> &ensp;&ensp; **pip install fastremap**\n",
     "> &ensp;&ensp; **pip install roifile**\n",
     "\n",
     "</div>"

diff --git a/stereo/image/segmentation_deepcell/seg_utils/cell_infer.py b/stereo/image/segmentation_deepcell/seg_utils/cell_infer.py
@@ -1,5 +1,4 @@
 import logging
-import os
 
 import numpy as np
 import tensorflow as tf
@@ -31,7 +30,7 @@ def __init__(self,
                  format_model_output_fn=None,
                  dataset_metadata=None,
                  model_metadata=None):
-        model_path = os.path.join(os.path.split(__file__)[0], 'model') if model is None else model
+        model_path = model
         self.model = tf.keras.models.load_model(model_path, compile=False)
         self.model_image_shape = self.model.input_shape[1:]
         # Require dimension 1 larger than model_input_shape due to addition of batch dimension

diff --git a/stereo/image/segmentation_deepcell/segment.py b/stereo/image/segmentation_deepcell/segment.py
@@ -48,8 +48,6 @@ def cell_seg_deepcell(
     ------------------
     None
     """
-    if version == 'v1' and not model_path:
-        raise Exception("cell_seg_deepcell() missing 1 required keyword argument: 'model_path'")
     try:
         import tensorflow as tf  # noqa
     except Exception: