Yuxiang Wang commited on
Commit
679611d
1 Parent(s): 438a207

add missing embedding files

Browse files
Files changed (3) hide show
  1. .gitignore +2 -0
  2. app.py +2 -1
  3. closest_sample.py +13 -2
.gitignore CHANGED
@@ -11,3 +11,5 @@ images/
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  model/
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  model_classification/
 
 
 
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  model/
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  model_classification/
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+ dataset/
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+ *.png
app.py CHANGED
@@ -111,7 +111,8 @@ with gr.Blocks(theme='sudeepshouche/minimalist') as demo:
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  classify_image_button = gr.Button("Classify Image")
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  with gr.Column():
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- segmented_image = gr.outputs.Image(label="SAM output",type='numpy')
 
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  segment_button = gr.Button("Segment Image")
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  #classify_segmented_button = gr.Button("Classify Segmented Image")
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  classify_image_button = gr.Button("Classify Image")
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  with gr.Column():
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+ #segmented_image = gr.outputs.Image(label="SAM output",type='numpy')
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+ segmented_image=gr.Image(label="Segmented Image", type='numpy')
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  segment_button = gr.Button("Segment Image")
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  #classify_segmented_button = gr.Button("Classify Segmented Image")
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closest_sample.py CHANGED
@@ -2,12 +2,23 @@ from sklearn.decomposition import PCA
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  import pickle as pk
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  import numpy as np
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  import pandas as pd
 
 
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  pca_fossils = pk.load(open('pca_fossils_170_finer.pkl','rb'))
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  pca_leaves = pk.load(open('pca_leaves_170_finer.pkl','rb'))
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- embedding_fossils = np.load('embedding_fossils_170_finer.npy')
 
 
 
 
 
 
 
 
 
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  #embedding_leaves = np.load('embedding_leaves.npy')
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  fossils_pd= pd.read_csv('fossils_paths.csv')
@@ -39,4 +50,4 @@ def get_images(embedding):
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  paths= [path.replace('/gpfs/data/tserre/irodri15/Fossils/new_data/leavesdb-v1_1/images/Fossil/Florissant_Fossil/512/full/jpg/',
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  '/media/data_cifs/projects/prj_fossils/data/processed_data/leavesdb-v1_1/images/Fossil/Florissant_Fossil/original/full/jpg/') for path in paths]
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  print(paths)
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- return paths
 
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  import pickle as pk
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  import numpy as np
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  import pandas as pd
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+ import os
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+ from huggingface_hub import snapshot_download
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  pca_fossils = pk.load(open('pca_fossils_170_finer.pkl','rb'))
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  pca_leaves = pk.load(open('pca_leaves_170_finer.pkl','rb'))
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+
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+ if not os.path.exists('dataset'):
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+ REPO_ID='Serrelab/Fossils'
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+ token = os.environ.get('READ_TOKEN')
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+ print(f"Read token:{token}")
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+ if token is None:
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+ print("warning! A read token in env variables is needed for authentication.")
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+ snapshot_download(repo_id=REPO_ID, token=token,repo_type='dataset',local_dir='dataset')
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+
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+ embedding_fossils = np.load('dataset/embedding_fossils_170_finer.npy')
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  #embedding_leaves = np.load('embedding_leaves.npy')
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  fossils_pd= pd.read_csv('fossils_paths.csv')
 
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  paths= [path.replace('/gpfs/data/tserre/irodri15/Fossils/new_data/leavesdb-v1_1/images/Fossil/Florissant_Fossil/512/full/jpg/',
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  '/media/data_cifs/projects/prj_fossils/data/processed_data/leavesdb-v1_1/images/Fossil/Florissant_Fossil/original/full/jpg/') for path in paths]
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  print(paths)
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+ return paths