Updated scripts

bowang-lab · Feb 28, 2025 · d1a4637 · d1a4637
1 parent bc54fe9
commit d1a4637
Show file tree

Hide file tree

Showing 4 changed files with 88 additions and 204 deletions.
diff --git a/morphodiff/evaluation/generate_img.py b/morphodiff/evaluation/generate_img.py
@@ -192,8 +192,7 @@ def load_model_and_generate_images(pipeline, model_checkpoint, prompts_df,
 
     # read perturbations
     prompts = []
-    perturbation_file = '../code/required_file/' +\
-        args.perturbation_list_address
+    perturbation_file = args.perturbation_list_address
 
     prompt_df = pd.read_csv(perturbation_file)
 

diff --git a/morphodiff/evaluation/perturbation_encoder.py b/morphodiff/evaluation/perturbation_encoder.py
@@ -3,14 +3,15 @@
 import numpy as np
 import torch
 import csv
+import os
 
 
 class PerturbationEncoder:
 
     def __init__(self, dataset_id, model_type, model_name):
         self.dataset_id = dataset_id
         self.model_type = model_type
-        self.root = "../required_file/"
+        self.root = os.path.dirname(os.path.abspath(__file__))+"/../required_file/"
 
         if 'HUVEC' in self.dataset_id:
             self.sirna_to_gene_df = pd.read_csv(
@@ -177,7 +178,7 @@ def __init__(self, dataset_id, model_type, model_name):
         self.dataset_id = dataset_id
         self.model_type = model_type
         self.model_name = model_name
-        self.root = "../code/required_file/"
+        self.root = os.path.dirname(os.path.abspath(__file__))+"/../required_file/"
 
         if 'HUVEC' in self.dataset_id:
             self.sirna_to_gene_df = pd.read_csv(

diff --git a/morphodiff/scripts/generate_img.sh b/morphodiff/scripts/generate_img.sh
@@ -20,12 +20,11 @@ trap 'handler' SIGUSR1
 ## Load the environment
 # source /home/env/morphodiff/bin/activate
 
-## Define/adjust the parameters
-EXPERIMENT="BBBC021-experiment-01-resized"
+## Define/adjust the parameters ##
+# Set the experiment name
+EXPERIMENT="BBBC021_experiment"
 # you can download pretrained checkpoints from https://huggingface.co/navidi/MorphoDiff_checkpoints/tree/main
 CKPT_PATH="/model/BBBC021-MorphoDiff/checkpoint-0"
-# For VAE, you can set path to the downloaded stable-diffusion-v1-4, or one of the pretrained chekcpoints
-VAE_PATH="/stable-diffusion-v1-4/"
 # Set path to the directory where you want to save the generated images
 GEN_IMG_PATH="/datasets/${EXPERIMENT}/generated_imgs/"
 # Set the number of images you want to generate
@@ -35,18 +34,19 @@ OOD=False
 MODEL_NAME="SD" # this is fixed
 MODEL_TYPE="conditional" # set "conditional" for MorphoDiff, and "naive" for unconditional SD
 
-# this PERTURBATION_LIST_PATH should be address of a .csv file with the following columns: perturbation, ood (including header)
-# sample file can be found in morphodiff/required_file/BBBC021_experiment_pert_ood_info.csv
-PERTURBATION_LIST_PATH="${EXPERIMENT}_pert_ood_info.csv" 
+# The PERTURBATION_LIST_PATH variable should be address of a .csv file with the following columns: perturbation, ood (including header)
+# sample file can be found in morphodiff/required_file/BBBC021_experiment_pert_ood_info.csv for the BBBC021 experiment sample, and
+# morphodiff/required_file/HUVEC_01_pert_ood_info.csv for the HUVEC experiment sample
+PERTURBATION_LIST_PATH="../required_file/${EXPERIMENT}_pert_ood_info.csv" 
 
 
 ## Generate images
-python evaluation/generate_img.py \
+python ../evaluation/generate_img.py \
 --experiment $EXPERIMENT \
 --model_checkpoint $CKPT_PATH \
 --model_name $MODEL_NAME \
 --model_type $MODEL_TYPE \
---vae_path $VAE_PATH \
+--vae_path $CKPT_PATH \
 --perturbation_list_address $PERTURBATION_LIST_PATH \
 --gen_img_path $GEN_IMG_PATH \
 --num_imgs $NUM_GEN_IMG \

diff --git a/requirements.txt b/requirements.txt
@@ -1,201 +1,85 @@
 absl-py==2.1.0
-accelerate==0.27.2
-aiohttp==3.9.3
-aiosignal==1.3.1
-annotated-types==0.6.0
-appdirs==1.4.4
-asttokens==2.4.1
-async-timeout==4.0.3
-attrs==23.2.0
-awscli==1.33.16
-botocore==1.34.134
-certifi==2024.2.2
-charset-normalizer==3.3.2
-chex==0.1.85
-cjm-pandas-utils==0.0.3
-cjm-pil-utils==0.0.9
-cjm-psl-utils==0.0.4
-cjm-pytorch-utils==0.0.6
-cjm-torchvision-tfms==0.0.11
-click==8.1.7
-colorama==0.4.6
-comm==0.2.2
-contourpy==1.2.0
-cycler==0.12.1
-datasets==2.18.0
-debugpy==1.8.1
-decorator==5.1.1
-deepspeed==0.13.5
-descriptastorus==2.6.1
-diffusers @ file:///fs01/home/znavidi/project/cell_painting/cell_painting_SD/code/diffusers
+accelerate==1.4.0
+aiohappyeyeballs==2.4.6
+aiohttp==3.11.13
+aiosignal==1.3.2
+annotated-types==0.7.0
+async-timeout==5.0.1
+attrs==25.1.0
+certifi==2025.1.31
+charset-normalizer==3.4.1
+click==8.1.8
+datasets==3.3.2
 dill==0.3.8
 docker-pycreds==0.4.0
-docutils==0.16
-dominate==2.9.1
-et-xmlfile==1.1.0
-etils==1.7.0
-exceptiongroup==1.2.0
-executing==2.0.1
-filelock==3.13.1
-flax==0.8.1
-fonttools==4.50.0
-frozenlist==1.4.1
-fsspec==2023.10.0
-ftfy==6.1.3
-gitdb==4.0.11
-GitPython==3.1.42
-greenlet==3.0.3
-grpcio==1.60.1
-h5py==3.10.0
-hjson==3.1.0
-huggingface-hub==0.20.3
-idna==3.6
-imageio==2.34.0
-imageio-ffmpeg==0.4.3
-importlib-metadata==7.0.1
-importlib_resources==6.1.3
-ipykernel==6.29.4
-ipython==8.23.0
-ipywidgets==8.1.2
-jax==0.4.25
-jaxlib==0.4.25
-jedi==0.19.1
-Jinja2==3.1.3
-jmespath==1.0.1
-joblib==1.4.0
-jsonpatch==1.33
-jsonpointer==3.0.0
-jupyter_client==8.6.1
-jupyter_core==5.7.2
-jupyterlab_widgets==3.0.10
-kaleido==0.2.1
-kiwisolver==1.4.5
-lazy_loader==0.3
-llvmlite==0.43.0
-Markdown==3.5.2
-markdown-it-py==3.0.0
-MarkupSafe==2.1.5
-matplotlib==3.8.3
-matplotlib-inline==0.1.6
-mdurl==0.1.2
-ml-dtypes==0.3.2
+filelock==3.17.0
+frozenlist==1.5.0
+fsspec==2024.12.0
+ftfy==6.3.1
+gitdb==4.0.12
+GitPython==3.1.44
+grpcio==1.70.0
+huggingface-hub==0.25.0
+idna==3.10
+importlib_metadata==8.6.1
+Jinja2==3.1.5
+Markdown==3.7
+MarkupSafe==3.0.2
 mpmath==1.3.0
-msgpack==1.0.8
-multidict==6.0.5
-multipledispatch==1.0.0
+multidict==6.1.0
 multiprocess==0.70.16
-mypy-extensions==1.0.0
-natsort==8.4.0
-nest-asyncio==1.6.0
-networkx==3.2.1
-ninja==1.11.1.1
-numba==0.60.0
-numpy==1.26.4
-nvidia-cublas-cu12==12.1.3.1
-nvidia-cuda-cupti-cu12==12.1.105
-nvidia-cuda-nvrtc-cu12==12.1.105
-nvidia-cuda-runtime-cu12==12.1.105
-nvidia-cudnn-cu12==8.9.2.26
-nvidia-cufft-cu12==11.0.2.54
-nvidia-curand-cu12==10.3.2.106
-nvidia-cusolver-cu12==11.4.5.107
-nvidia-cusparse-cu12==12.1.0.106
-nvidia-nccl-cu12==2.19.3
-nvidia-nvjitlink-cu12==12.3.101
-nvidia-nvtx-cu12==12.1.105
-opencv-python==4.9.0.80
-openpyxl==3.1.5
-opt-einsum==3.3.0
-optax==0.2.0
-orbax-checkpoint==0.5.3
-packaging==23.2
-pandas==2.2.0
-pandas-flavor==0.6.0
-parso==0.8.4
+networkx==3.4.2
+numpy==2.2.3
+nvidia-cublas-cu12==12.4.5.8
+nvidia-cuda-cupti-cu12==12.4.127
+nvidia-cuda-nvrtc-cu12==12.4.127
+nvidia-cuda-runtime-cu12==12.4.127
+nvidia-cudnn-cu12==9.1.0.70
+nvidia-cufft-cu12==11.2.1.3
+nvidia-curand-cu12==10.3.5.147
+nvidia-cusolver-cu12==11.6.1.9
+nvidia-cusparse-cu12==12.3.1.170
+nvidia-cusparselt-cu12==0.6.2
+nvidia-nccl-cu12==2.21.5
+nvidia-nvjitlink-cu12==12.4.127
+nvidia-nvtx-cu12==12.4.127
+packaging==24.2
+pandas==2.2.3
 peft==0.7.0
-pexpect==4.9.0
-pillow==10.2.0
-platformdirs==4.2.0
-plotly==5.24.1
-prompt-toolkit==3.0.43
-protobuf==4.25.3
-psutil==5.9.8
-ptyprocess==0.7.0
-pure-eval==0.2.2
-py-cpuinfo==9.0.0
-pyarrow==15.0.0
-pyarrow-hotfix==0.6
-pyasn1==0.6.0
-pybbbc @ git+https://github.com/giacomodeodato/pybbbc.git@27d6289d231f869561e0515ecce4934a8e744f39
-pycytominer==1.1.0
-pydantic==2.6.3
-pydantic_core==2.16.3
-Pygments==2.17.2
-pyjanitor==0.27.0
-pynndescent==0.5.13
-pynvml==11.5.0
-pyparsing==3.1.2
-pyre-extensions==0.0.30
-pyspng==0.1.2
-python-dateutil==2.8.2
-pytz==2024.1
-PyYAML==6.0.1
-pyzmq==25.1.2
-rdkit==2023.9.5
-regex==2023.12.25
-requests==2.31.0
-rich==13.7.1
-rsa==4.7.2
-s3transfer==0.10.2
-safetensors==0.4.2
-scikit-image==0.22.0
-scikit-learn==1.4.2
-scipy==1.11.1
-seaborn==0.13.2
-sentry-sdk==1.44.0
-setproctitle==1.3.3
-six==1.16.0
-smmap==5.0.1
-SQLAlchemy==1.4.53
-stack-data==0.6.3
-swd==1.0.0
-sympy==1.12
-tabulate==0.9.0
-tenacity==9.0.0
-tensorboard==2.16.2
+pillow==11.1.0
+platformdirs==4.3.6
+propcache==0.3.0
+protobuf==5.29.3
+psutil==7.0.0
+pyarrow==19.0.1
+pydantic==2.10.6
+pydantic_core==2.27.2
+python-dateutil==2.9.0.post0
+pytz==2025.1
+PyYAML==6.0.2
+regex==2024.11.6
+requests==2.32.3
+safetensors==0.5.3
+sentry-sdk==2.22.0
+setproctitle==1.3.5
+six==1.17.0
+smmap==5.0.2
+sympy==1.13.1
+tensorboard==2.19.0
 tensorboard-data-server==0.7.2
-tensorstore==0.1.54
-thop==0.1.1.post2209072238
-threadpoolctl==3.5.0
-tifffile==2024.2.12
-timm==1.0.8
 tokenizers==0.15.2
-toolz==0.12.1
-torch==2.2.1
-torch-fidelity==0.3.0
-torcheval==0.0.7
-torchtnt==0.2.4
-torchvision==0.17.1
-tornado==6.4
-tqdm==4.66.2
-traitlets==5.14.2
+torch==2.6.0
+torchvision==0.21.0
+tqdm==4.67.1
 transformers==4.38.2
-triton==2.2.0
-typing-inspect==0.9.0
-typing_extensions==4.9.0
-tzdata==2024.1
-ultralytics==8.1.38
-umap-learn==0.5.6
-urllib3==2.2.1
-visdom==0.2.4
-wandb==0.16.5
+triton==3.2.0
+typing_extensions==4.12.2
+tzdata==2025.1
+urllib3==2.3.0
+wandb==0.19.7
 wcwidth==0.2.13
-websocket-client==1.8.0
-Werkzeug==3.0.1
-widgetsnbextension==4.0.10
-xarray==2024.3.0
-xformers==0.0.24
-XlsxWriter==3.2.0
-xxhash==3.4.1
-yarl==1.9.4
-zipp==3.17.0
+Werkzeug==3.1.3
+xformers @ git+https://github.com/facebookresearch/xformers.git@91b8f8d19d02d4bc643c89031905caf0c3e73382
+xxhash==3.5.0
+yarl==1.18.3
+zipp==3.21.0