Merge pull request #144 from linok-bc/master

pytc docs update

Author: donglaiw

.readthedocs.yaml

@@ -5,6 +5,17 @@
 # Required
 version: 2
 
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-22.9"
+  commands:
+    - mamba env create --quiet --name latest --file docs/environment_docs.yml
+    - pip install --editable .
+    - git clone https://github.com/pytorch/pytorch_sphinx_theme
+    - pip install -e pytorch_sphinx_theme
+    - python -m sphinx -T -b html -d _build/doctrees -D language=en ./docs/source $READTHEDOCS_OUTPUT/html
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py

configs/CREMI/CREMI-Base.yaml

@@ -1,24 +1,24 @@
 # All other configurations are set by default. If you want to add new config options,
 # please modify ../connectomics/config/defaults.py
 SYSTEM:
-  NUM_GPUS: 3
-  NUM_CPUS: 12
+  NUM_GPUS: 1
+  NUM_CPUS: 1
 MODEL:
   INPUT_SIZE: [17, 257, 257]
   OUTPUT_SIZE: [17, 257, 257]
   IN_PLANES: 1
   NORM_MODE: sync_bn
   FILTERS: [32, 64, 96, 128, 160]
 DATASET:
-  IMAGE_NAME: images/im_A_v2_200.h5@images/im_B_v2_200.h5@images/im_C_v2_200.h5
-  LABEL_NAME: gt-syn/syn_A_v2_200.h5@gt-syn/syn_B_v2_200.h5@gt-syn/syn_C_v2_200.h5
+  IMAGE_NAME: corrected/im_A.h5@corrected/im_B.h5@corrected/im_C.h5
+  LABEL_NAME: corrected/syn_A.h5@corrected/syn_B.h5@corrected/syn_C.h5
   INPUT_PATH: datasets/CREMI/
   OUTPUT_PATH: outputs/CREMI_syn_baseline
   PAD_SIZE: [0, 32, 32]
   REJECT_SAMPLING:
     SIZE_THRES: 1000
     P: 0.95
-  DISTRIBUTED: True
+  DISTRIBUTED: False
 SOLVER:
   LR_SCHEDULER_NAME: WarmupCosineLR
   BASE_LR: 0.02
@@ -30,7 +30,7 @@ INFERENCE:
   INPUT_SIZE: [17, 257, 257]
   OUTPUT_SIZE: [17, 257, 257]
   OUTPUT_ACT: ["sigmoid"]
-  IMAGE_NAME: images/im_A+_v2_200_nocrack.h5@images/im_B+_v2_200.h5@images/im_C+_v2_200.h5
+  IMAGE_NAME: corrected/im_A+.h5@corrected/im_B+.h5@corrected/im_C+.h5
   OUTPUT_PATH: outputs/CREMI_syn_baseline/test
   OUTPUT_NAME: result.h5
   DO_SINGLY: True

configs/CREMI/CREMI-Base_multiGPU.yaml

@@ -0,0 +1,41 @@
+# All other configurations are set by default. If you want to add new config options,
+# please modify ../connectomics/config/defaults.py
+SYSTEM:
+  NUM_GPUS: 3
+  NUM_CPUS: 12
+MODEL:
+  INPUT_SIZE: [17, 257, 257]
+  OUTPUT_SIZE: [17, 257, 257]
+  IN_PLANES: 1
+  NORM_MODE: sync_bn
+  FILTERS: [32, 64, 96, 128, 160]
+DATASET:
+  IMAGE_NAME: corrected/im_A.h5@corrected/im_B.h5@corrected/im_C.h5
+  LABEL_NAME: corrected/syn_A.h5@corrected/syn_B.h5@corrected/syn_C.h5
+  INPUT_PATH: datasets/CREMI/
+  OUTPUT_PATH: outputs/CREMI_syn_baseline
+  PAD_SIZE: [0, 32, 32]
+  REJECT_SAMPLING:
+    SIZE_THRES: 1000
+    P: 0.95
+  DISTRIBUTED: True
+SOLVER:
+  LR_SCHEDULER_NAME: WarmupCosineLR
+  BASE_LR: 0.02
+  ITERATION_STEP: 1
+  ITERATION_SAVE: 5000
+  ITERATION_TOTAL: 150000
+  SAMPLES_PER_BATCH: 2
+INFERENCE:
+  INPUT_SIZE: [17, 257, 257]
+  OUTPUT_SIZE: [17, 257, 257]
+  OUTPUT_ACT: ["sigmoid"]
+  IMAGE_NAME: corrected/im_A+.h5@corrected/im_B+.h5@corrected/im_C+.h5
+  OUTPUT_PATH: outputs/CREMI_syn_baseline/test
+  OUTPUT_NAME: result.h5
+  DO_SINGLY: True
+  PAD_SIZE: [0, 32, 32]
+  AUG_MODE: mean
+  AUG_NUM: 8
+  STRIDE: [8, 128, 128]
+  SAMPLES_PER_BATCH: 8

configs/SNEMI/SNEMI-Base.yaml

@@ -1,8 +1,8 @@
 # All other configurations are set by default. If you want to add new config options,
 # please modify ../connectomics/config/defaults.py
 SYSTEM:
-  NUM_GPUS: 2
-  NUM_CPUS: 16
+  NUM_GPUS: 1
+  NUM_CPUS: 1
 AUGMENTOR:
   SMOOTH: False
 MODEL:
@@ -19,8 +19,8 @@ MODEL:
   FILTERS: [32, 64, 96, 128, 160]
   NORM_MODE: gn
 DATASET:
-  IMAGE_NAME: train_image.h5
-  LABEL_NAME: train_label.h5
+  IMAGE_NAME: train-input.tif
+  LABEL_NAME: train-label.tif
   INPUT_PATH: datasets/SNEMI3D/ # or your own dataset path
   OUTPUT_PATH: outputs/SNEMI3D/
   PAD_SIZE: [4, 64, 64]

configs/SNEMI/SNEMI-Base_multiGPU.yaml

@@ -0,0 +1,47 @@
+# All other configurations are set by default. If you want to add new config options,
+# please modify ../connectomics/config/defaults.py
+SYSTEM:
+  NUM_GPUS: 2
+  NUM_CPUS: 16
+AUGMENTOR:
+  SMOOTH: False
+MODEL:
+  INPUT_SIZE: [17, 257, 257]
+  OUTPUT_SIZE: [17, 257, 257]
+  IN_PLANES: 1
+  OUT_PLANES: 3
+  TARGET_OPT: ["2"]
+  LABEL_EROSION: 1
+  LOSS_OPTION: [["WeightedBCEWithLogitsLoss", "DiceLoss"]]
+  LOSS_WEIGHT: [[1.0, 0.5]]
+  WEIGHT_OPT: [["1", "0"]]
+  OUTPUT_ACT: [["none", "sigmoid"]]
+  FILTERS: [32, 64, 96, 128, 160]
+  NORM_MODE: gn
+DATASET:
+  IMAGE_NAME: train-image.tif
+  LABEL_NAME: train-label.tif
+  INPUT_PATH: datasets/SNEMI3D/ # or your own dataset path
+  OUTPUT_PATH: outputs/SNEMI3D/
+  PAD_SIZE: [4, 64, 64]
+SOLVER:
+  LR_SCHEDULER_NAME: WarmupCosineLR
+  BASE_LR: 0.02
+  ITERATION_STEP: 1
+  ITERATION_SAVE: 10000
+  ITERATION_TOTAL: 150000
+  SAMPLES_PER_BATCH: 2
+MONITOR:
+  ITERATION_NUM: [200, 1000]
+INFERENCE:
+  INPUT_SIZE: [17, 513, 513]
+  OUTPUT_SIZE: [17, 513, 513]
+  OUTPUT_ACT: ["sigmoid"]
+  IMAGE_NAME: test-input.tif # or path to your test images
+  OUTPUT_PATH: outputs/SNEMI3D/test
+  OUTPUT_NAME: result.h5
+  PAD_SIZE: [4, 32, 32]
+  AUG_MODE: min
+  AUG_NUM: None
+  STRIDE: [8, 256, 256]
+  SAMPLES_PER_BATCH: 4

docs/README.md

@@ -1,5 +1,11 @@
 To update the documentation
 
-1. Install packages: `pip install -r requirements.txt`
-2. Modify source files in `source/`
-3. Compile the code: `make html`
+1. Install connectomics package
+2. Install docs package: `pip install -r requirements.txt`
+3. Install correct version of pytorch_sphinx_theme: 
+```
+    git clone https://github.com/pytorch/pytorch_sphinx_theme
+    pip install -e pytorch_sphinx_theme
+```
+4. Modify source files in `source/`
+5. Compile the code: `make html`