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params.py
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class PromptLearnerConfig():
def __init__(self, n_ctx=32, input_size=256, ctx_init="a histopathology image showing"):
self.model_backbone_name = "ViT-B/16"
self.n_ctx = n_ctx
self.ctx_init = ctx_init
#self.ctx_init = ''
#self.ctx_ini = 'a histopathology image showing a histopathology image showing a histopathology image showing a histopathology image showing a histopathology image showing a histopathology image showing a histopathology image showing a histopathology image showing'
self.input_size = [input_size]
# self.csc = False
self.token_embedding_size = 768
CKPT_PATH = "/ailab/group/pjlab-medai/zhouxiao/pathology/model/conch/pytorch_model.bin"
LOCAL_CKPT_PATH = "C:\\Users\\Administrator\\Code\\pathology\\model\\conch\\pytorch_model.bin"
KEEP_PATH = '/ailab/group/pjlab-medai/zhouxiao/pathology/model/keep'
TESTSET_DIVISION = "/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/testset_division.json"
TRAINSET_DIVISION = "/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/trainset_division.json"
SAVE_DIR = "/ailab/user/sunluoyi/HEDEXUAN/myCoOp/prompt/"
DATASET_DIVISION = '/ailab/group/pjlab-medai/zhouxiao/pathology/data/tcga_WSI_data/dataset_division.json'
CM_det = {
'train_dir_path' : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/CM/CM_train",
'test_dir_path' : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/CM/CM_test",
'train_label_csv' : "/ailab/group/pjlab-medai/zhouxiao/pathology/data/cptac_WSI_data/CM_meta.csv",
'test_label_csv' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/cptac_WSI_data/cptac_cm_detection.csv',
'zero_shot_template_file' : "/ailab/group/pjlab-medai/zhouxiao/pathology/prompts/detection/cptac_cm_prompts_all.json",
'testset_ids' : ["C3L-02622-23","C3N-02270-23","C3N-01844-26","C3N-03614-26","C3N-03097-25","C3N-02270-21","C3L-05299-25","C3N-02330-23","C3N-02324-26","C3L-03382-26","C3N-02324-21","C3L-02647-27","C3N-04142-21","C3N-02026-26","C3L-04732-26","C3N-03885-26","C3L-02647-28","C3N-02270-25","C3N-03229-21","C3L-06113-21","C3L-05262-26","C3N-02373-26","C3N-02327-23","C3L-04331-28","C3N-01495-27","C3N-00209-27","C3L-06110-22","C3L-04212-25","C3N-03239-21","C3N-03239-26","C3N-00209-24","C3N-05624-25","C3N-02330-21","C3N-00179-21","C3L-02647-26","C3N-03229-23","C3N-03097-27","C3N-03223-26","C3N-00378-21","C3N-01493-27","C3L-00967-27","C3L-04212-27","C3L-02622-26","C3N-03916-21","C3L-05262-22","C3L-02615-23","C3L-05517-22","C3L-00629-23","C3L-05302-28","C3L-04207-26","C3L-04331-25","C3N-02335-22","C3L-01063-26","C3N-02040-26","C3L-03381-24","C3N-03220-21","C3N-00376-21","C3N-01824-23","C3N-03918-21","C3N-01530-26","C3L-05781-26","C3L-03381-23","C3N-00376-23","C3N-00874-25","C3N-00434-23","C3N-02040-21","C3N-02633-21","C3N-02373-22","C3L-04760-26","C3L-05302-26","C3N-03228-26","C3N-03097-26","C3L-05302-22","C3L-05262-27","C3L-05027-22","C3N-01493-22","C3N-02324-23","C3L-05554-21","C3L-04331-24","C3N-03235-21","C3L-05229-26","C3L-05527-23","C3N-00179-26","C3N-04294-21","C3L-01063-23","C3N-04156-22","C3L-05781-21","C3N-00220-26","C3L-04212-26","C3N-01533-22","C3N-03229-26","C3L-05175-26","C3L-03367-22","C3N-00179-27","C3N-02324-22","C3N-01492-26","C3N-03913-23","C3N-00327-26","C3N-05623-24","C3N-00384-26","C3L-04739-22","C3L-05299-28","C3N-02679-22","C3L-05517-23","C3N-00209-21","C3L-04739-27","C3L-04212-24","C3N-00378-26","C3L-06113-22","C3L-04733-26","C3L-02102-28","C3N-03916-22","C3N-03913-21","C3N-02270-22","C3L-04787-22","C3L-05299-24","C3N-00432-26","C3L-00967-24","C3N-00376-24","C3L-02622-29","C3N-00385-25","C3N-00220-22","C3L-03381-25","C3N-01481-24","C3N-00209-26","C3N-01533-26","C3L-03364-30","C3N-01481-23","C3L-06113-23","C3N-04156-23","C3N-01494-27","C3N-02335-23","C3L-05262-28","C3N-03918-26","C3L-04739-28","C3L-00989-21","C3N-00434-21","C3N-03916-26","C3N-02335-26","C3N-03220-26","C3N-03097-28","C3L-03362-24","C3L-03377-23","C3N-03234-22","C3N-01492-21","C3N-01845-21","C3L-00967-26","C3L-00967-21","C3L-04739-21","C3N-00434-26"],
'batch_size': 1024,
}
CM_det_local = {
'train_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\CM\\h5_files\\train",
'test_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\CM\\h5_files\\test",
'train_label_csv' : "C:\\Users\\Administrator\\Code\\pathology\\data\\cptac_meta\\CM_meta.csv",
'test_label_csv' : 'C:\\Users\\Administrator\\Code\\pathology\\data\\CM\\cptac_cm_detection.csv',
'zero_shot_template_file' : "C:\\Users\\Administrator\\Code\\pathology\\data\\prompts\\detection\\cptac_cm_prompts_all.json",
'batch_size': 512,
}
camelyon_det = {
'tumor_dir_path' : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/camelyon/tumor/h5_files",
'normal_dir_path' : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/camelyon/normal/h5_files",
'zero_shot_template_file' : "/ailab/group/pjlab-medai/zhouxiao/pathology/prompts/segment/other_camelyon_tumor_prompts_all.json",
'batch_size': 1024,
}
camelyon_seg = {
'tumor_dir_path' : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/camelyon/tumor/h5_files",
'normal_dir_path' : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/camelyon/normal/h5_files",
'mask_dir_path' : "/ailab/group/pjlab-medai/zhouxiao/pathology/data/other_WSI_data/camelyon_tumor/test/tumor_masks",
'patch_mask_dir_path' : "/ailab/user/sunluoyi/HEDEXUAN/myCoOp/gen_patch_masks/camelyon/patch_masks",
'zero_shot_template_file' : "/ailab/group/pjlab-medai/zhouxiao/pathology/prompts/segment/other_camelyon_tumor_prompts_all.json",
'testset_ids' : ['test_071','test_026','test_079','test_065','test_010','test_051','test_104','test_002','test_094','test_013','test_121','test_029','test_001','test_030','test_084','test_099','test_102','test_108','test_110','test_068','test_117','test_064','test_122','test_011'],
'batch_size': 1024,
}
camelyon_det_local = {
'tumor_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\camelyon\\tumor\\h5_files",
'normal_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\camelyon\\normal\\h5_files",
'zero_shot_template_file' : "C:\\Users\\Administrator\\Code\\pathology\\data\\prompts\\segment\\other_camelyon_tumor_prompts_all.json",
'batch_size': 1024,
}
camelyon_seg_local = {
'tumor_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\camelyon\\tumor\\h5_files",
'normal_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\camelyon\\normal\\h5_files",
'mask_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\data\\camelyon\\tumor_masks",
'patch_mask_dir_path' : "C:\\Users\\Administrator\\Code\\pathology\\data\\camelyon\\patch_masks",
'zero_shot_template_file' : "C:\\Users\\Administrator\\Code\\pathology\\data\\prompts\\segment\\other_camelyon_tumor_prompts_all.json",
'testset_ids' : ['test_071','test_026','test_079','test_065','test_010','test_051','test_104','test_002','test_094','test_013','test_121','test_029','test_001','test_030','test_084','test_099','test_102','test_108','test_110','test_068','test_117','test_064','test_122','test_011'],
'batch_size': 1024,
}
gbmlgg_sub = {
"source":'TCGA',
"gbm_dir_path" : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/GBM_test/h5_files",
"lgg_dir_path" : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/LGG_test/h5_files",
"label_csv" : "/ailab/group/pjlab-medai/zhouxiao/pathology/data/tcga_WSI_data/tcga_brain_test.csv",
"zero_shot_template_file" : "/ailab/group/pjlab-medai/zhouxiao/pathology/prompts/subtyping/tcga_brain_prompts_all.json",
'testset_ids' : ['TCGA-HT-7478-01Z-00-DX1.B3835ABC-63FC-4AEA-B874-5701429C65B7', 'TCGA-CS-4938-01Z-00-DX1.6660D726-8524-424A-B6E8-D97FFD9BCE01', 'TCGA-FG-8185-01Z-00-DX1.99b9779e-d967-47c6-836c-8b71a335b9a0', 'TCGA-P5-A736-01Z-00-DX1.FCED7667-57E1-4064-89EB-75DF60076945', 'TCGA-HW-8320-01Z-00-DX1.71FC4C29-1D2A-4227-82B9-9D59A9AF38A0', 'TCGA-HT-A4DS-01Z-00-DX2.178ADC93-3630-43D3-B248-915764105CEC', 'TCGA-DU-5854-01Z-00-DX1.b4d00993-a322-4d5a-b7a1-06db7ad078ab', 'TCGA-DU-A5TP-01Z-00-DX1.93C7592D-91A7-4A89-96A8-190654A36BA9', 'TCGA-S9-A7IX-01Z-00-DX1.41EFC469-2139-44A6-AE48-76304EBD3F58', 'TCGA-FG-A87Q-01Z-00-DX3.426D47B6-2D6C-4F6E-9546-2E121A9DDAB2', 'TCGA-DU-5847-01Z-00-DX1.b7d7de58-38b6-4686-8588-a2542c8595b4', 'TCGA-S9-A6U9-01Z-00-DX1.320C7173-3FAF-4661-8C0D-2C7B46BF17D9', 'TCGA-S9-A6WM-01Z-00-DX1.5D18F7F7-C5C8-465B-8B7D-FAC68C43C6F5', 'TCGA-E1-A7Z3-01Z-00-DX1.1CB2A0F0-0A5C-4DD1-8CD9-8FDBD0CAEC74', 'TCGA-TM-A7CF-01Z-00-DX1.EB905EDB-5AC5-41C4-AB00-526DD3820524', 'TCGA-CS-4943-01Z-00-DX1.42332d6f-e16e-40ae-a629-69c537d79465', 'TCGA-S9-A6WO-01Z-00-DX1.7B2357DB-9EF4-4122-9A7E-F6F509A0A67C', 'TCGA-DB-5277-01Z-00-DX1.635F8997-B57B-402D-8889-BE84CA858B16', 'TCGA-TM-A84B-01Z-00-DX1.8736E13D-D47F-462E-BD06-61767245C2F5', 'TCGA-VV-A86M-01Z-00-DX1.3D542AC0-4000-40AA-A574-791B8772F956', 'TCGA-WY-A859-01Z-00-DX1.650758FF-1BE8-4A56-8A9A-319BA0363D8F', 'TCGA-DU-6392-01Z-00-DX1.f44c08a3-d488-483d-b760-f23b0160f832', 'TCGA-E1-A7YJ-01Z-00-DX1.199900DB-6829-49BB-B139-9C344BD4D810', 'TCGA-DU-A76O-01Z-00-DX1.79424261-499C-4D61-9C74-3A35E1557501', 'TCGA-HT-7604-01Z-00-DX1.6889187F-B89A-4CC0-8224-709DFF523FEE', 'TCGA-TM-A84I-01Z-00-DX1.755573F1-0378-4E95-A755-CD8AB79ABEC1', 'TCGA-FG-5963-01Z-00-DX1.7bcacb10-cec1-4397-9c3a-bf08cab7d63d', 'TCGA-DH-5142-01Z-00-DX1.3C7EAF01-4DC5-4FBE-849D-17DD3A6B5D8D', 'TCGA-HW-7490-01Z-00-DX1.2109dc98-1288-4da2-963e-4544db680603', 'TCGA-E1-A7Z4-01Z-00-DX2.4DFFB8EE-BE6E-46F0-AC6D-8CC65BDA9441', 'TCGA-HT-A5R7-01Z-00-DX1.710C776B-5420-42E6-8D40-C5C36D1CA603', 'TCGA-HT-A61B-01Z-00-DX1.4D520756-D42C-480F-B13A-E2D6B4421668', 'TCGA-S9-A6TZ-01Z-00-DX1.5D0335F4-DB48-4428-800F-2B27E431BAA8', 'TCGA-HT-A5RC-01Z-00-DX1.6E1C0CF0-7D7D-4F5B-8D65-451AA9AE8B61', 'TCGA-P5-A781-01Z-00-DX1.98EFF9A5-448D-47DD-848B-29DBD40FC453', 'TCGA-DU-6405-01Z-00-DX1.f5511a52-10ce-458d-a810-cd9c7fb1a0c6', 'TCGA-HT-7476-01Z-00-DX3.BA9C415D-34F0-4122-BC9A-3E7A57502D19', 'TCGA-HT-8012-01Z-00-DX1.6437C769-CD18-4DC2-8961-1E2C89018045', 'TCGA-HT-7469-01Z-00-DX1.53A588BD-3B74-4DB6-BE8D-A6E80119E3EB', 'TCGA-TM-A84O-01Z-00-DX1.C05AE734-FABD-4DA7-9FDA-A54564CDED27', 'TCGA-R8-A73M-01Z-00-DX1.F73016FC-3180-4D90-9D49-2FA04F9BC5A3', 'TCGA-QH-A65Z-01Z-00-DX1.33A27DCF-3B96-468B-AF2C-6F394EFA44EF', 'TCGA-HT-8010-01Z-00-DX1.43C29B1E-B4D4-451A-8ACC-44C016FAB6FC', 'TCGA-HW-8322-01Z-00-DX1.B6F32F6B-7FA3-42E4-98CB-F2F55208F7C4', 'TCGA-FG-A6J1-01Z-00-DX1.F360DE20-12F7-4727-8A21-C3D3F3EA4AF2', 'TCGA-DH-5141-01Z-00-DX1.26FDB9A2-CCA7-4B0C-9743-3C4E140B31D7', 'TCGA-HT-A4DV-01Z-00-DX2.702EF31E-4E34-482D-AE05-3EDEED527CAA', 'TCGA-HT-A615-01Z-00-DX1.454CE5AA-213B-4479-B6B9-4CEAB6EC951A', 'TCGA-DH-A7UR-01Z-00-DX1.CD0C3921-255F-4415-BE61-240068DD1C9D', 'TCGA-FG-7634-01Z-00-DX1.BF0F2F3E-2CAD-495C-A0E6-D8194BCC4A77', 'TCGA-DH-5144-01Z-00-DX1.4DBB9F00-3215-4199-B8D6-16CC5E517E6F', 'TCGA-DU-A7TG-01Z-00-DX1.BB74AF60-791A-42D8-8798-8BCEF80F3C1D', 'TCGA-HW-7491-01Z-00-DX1.0648acf5-5dbd-47ad-96fd-52d765398718', 'TCGA-HT-7689-01Z-00-DX3.8AE3ABC7-70E8-4804-94B2-C274ACBCA2CC', 'TCGA-P5-A72Z-01Z-00-DX1.096F894F-C7EE-4CBC-A024-26B4513126A7', 'TCGA-HT-7605-01Z-00-DX1.CDE02BA4-CE97-4542-BB96-C3D568A32217', 'TCGA-CS-5396-01Z-00-DX1.63f3413b-a950-417a-a49e-9d01efe45c88', 'TCGA-TQ-A7RF-01Z-00-DX1.0243E73B-9B79-46C0-BA92-E8BA46E56036', 'TCGA-DH-A66G-01Z-00-DX1.82A4242B-EAB4-4474-B5C9-27FD5C322201', 'TCGA-DU-6399-01Z-00-DX1.1a964643-a0f0-4338-8976-3bf5f832236c', 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'TCGA-12-0769-01Z-00-DX6.093886ef-289d-45af-a327-457877628447', 'TCGA-12-1602-01Z-00-DX5.699D9FC4-F113-4DC5-8DCB-B00150AA8B98', 'TCGA-06-0184-01Z-00-DX3.05b0e8e2-9a0a-460f-a7f7-f87a425ad1f1', 'TCGA-06-5418-01Z-00-DX1.8c45ebb4-528d-4d2d-bde0-05266b51f06c', 'TCGA-27-2519-01Z-00-DX1.C630FE42-2691-4735-83EB-6F78AAA407B3', 'TCGA-26-5135-01Z-00-DX1.928F0E13-33FE-4669-9DCE-A53654D99764', 'TCGA-26-5133-01Z-00-DX1.DE65E680-153B-4A6F-991B-6CCC58F39CF1', 'TCGA-14-1453-01Z-00-DX3.d85f42df-ac7e-45b5-807e-929204bf3c87', 'TCGA-12-0691-01Z-00-DX4.f7c6d2db-9c2d-4cfb-ba31-6392599c561a', 'TCGA-02-0024-01Z-00-DX1.d4cec60d-e2b6-41d1-92af-2d24f15b03a9', 'TCGA-27-1838-01Z-00-DX1.3ada1ada-fb14-4761-84f9-66a339e86e73', 'TCGA-06-0137-01Z-00-DX3.84d2c007-be53-431d-b5d6-1bb62d28cafb', 'TCGA-28-1745-01Z-00-DX1.44d465d5-453d-4c06-85db-14de0656f0b3', 'TCGA-02-0430-01Z-00-DX1.aa4aaacb-1f80-48f3-84c0-39accafc45a7', 'TCGA-08-0354-01Z-00-DX1.577F7E82-1CDD-4639-9079-AC24FCE94BF7', 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'TCGA-06-5411-01Z-00-DX1.08bf7f79-7346-4b1b-b8a7-e24abf11e848', 'TCGA-08-0520-01Z-00-DX1.2d50b1bc-c1d8-41a4-b42f-19d9916a5ef6', 'TCGA-08-0531-01Z-00-DX1.94295471-3786-4561-9AE7-4643A4C14DF4', 'TCGA-19-5956-01Z-00-DX1.f50d2a6f-1937-48ac-b198-e6d70870c75c', 'TCGA-06-0644-01Z-00-DX1.bbce7e5c-6df3-4963-ac75-9f566a2fde12', 'TCGA-06-0208-01Z-00-DX1.cea28355-3b64-48e6-b5f7-9a0d2b319150'],
"batch_size": 4096,
"patch_num": 4096,
"loss_type": 'patch',
"log_name":'patch_2e-4_e20',
}
shenmu_sub = {
"source":'xinhua',
"h5_dir_path" : "/ailab/user/zhouxiao/xinhua_feats/conch/shenmu_all/h5_files",
"train_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_shenmu_all_subtyping_train.csv",
"test_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_shenmu_all_subtyping_test.csv",
"zero_shot_template_file" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/prompts/shenmu_all_prompts.json",
"subtype_names": ['Ganglioneuroblastoma, intermixed', 'Differentiating neuroblastoma', 'Poorly differentiated neuroblastoma'],
"batch_size": 4096,
"patch_num": 4096,
"loss_type": 'patch',
"log_name":'shenmu_patch_2e-4',
}
suimu_sub = {
"source":'xinhua',
"h5_dir_path" : "/ailab/user/zhouxiao/xinhua_feats/conch/suimu_all/h5_files",
"train_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_suimu_all_subtyping_train.csv",
"test_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_suimu_all_subtyping_test.csv",
"zero_shot_template_file" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/prompts/suimu_all_prompts.json",
"subtype_names": ['Large Cell/Anaplastic medulloblastoma', 'Desmoplastic nodular medulloblastoma', 'Classic medulloblastoma'],
"batch_size": 4096,
"patch_num": 4096,
"loss_type": 'patch',
"log_name":'suimu_patch_2e-4',
}
ganmu_sub = {
"source":'xinhua',
"h5_dir_path" : "/ailab/user/zhouxiao/xinhua_feats/conch/ganmu_all/h5_files",
"train_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_ganmu_all_subtyping_train.csv",
"test_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_ganmu_all_subtyping_test.csv",
"zero_shot_template_file" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/prompts/ganmu_all_prompts.json",
"subtype_names": ['Epithelial macrotrabecular pattern of hepatoblastoma', 'Mixed epithelial and mesenchymal hepatoblastoma', 'Epithelial mixed fetal and embryonal hepatoblastoma', 'Pure fetal hepatoblastoma with low mitotic activity'],
"batch_size": 4096,
"patch_num": 4096,
"loss_type": 'patch',
"log_name":'ganmu_patch_2e-4',
}
shenzangmu_sub = {
"source":'xinhua',
"h5_dir_path" : "/ailab/user/zhouxiao/xinhua_feats/conch/shenzangmu_all/h5_files",
"train_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_shenzangmu_all_subtyping_train.csv",
"test_label_csv" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/data_csvs/fewshot_shenzangmu_all_subtyping_test.csv",
"zero_shot_template_file" : "/ailab/user/zhouxiao/WSI_proc_code/MI-Zero-main/xinhua_src/prompts/shenzangmu_all_prompts.json",
"subtype_names": ['nephroblastoma, blastemal type', 'nephroblastoma, stromal type','mixed blastemal and epithelial nephroblastoma','mixed blastemal and stromal nephroblastoma','mixed blastemal, epithelial and stromal nephroblastoma'],
"batch_size": 4096,
"patch_num": 4096,
"loss_type": 'patch',
"log_name":'shenzangmu_patch_2e-4',
}
gbmlgg_sub_local = {
"gbm_dir_path" : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\GBM\\test\\h5_files",
"lgg_dir_path" : "C:\\Users\\Administrator\\Code\\pathology\\features\\conch\\LGG\\test\\h5_files",
"label_csv" : "C:\\Users\\Administrator\\Code\\pathology\\data\\cptac_meta\\tcga_brain_test.csv",
"zero_shot_template_file" : "C:\\Users\\Administrator\\Code\\pathology\\data\\prompts\\subtyping\\tcga_brain_prompts_all.json",
"batch_size": 1024,
}
patchcamelyon_cls = {
"zero_shot_template_file" : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Patchcamelyon/Patchcamelyon_prompts_100.json',
"train_data_dir" : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Patchcamelyon/train/images',
"train_label_csv" : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Patchcamelyon/train/labels.csv',
'test_data_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/patchCamelyon/test.pt',
'test_label_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/patchCamelyon/test_label.pt',
'valid_data_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/patchCamelyon/valid.pt',
'valid_label_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/conch/patchCamelyon/valid_label.pt'
}
bach_cls = {
'label_csv' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Bach/Bach_test.csv',
'train_data_dir' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Bach/images_224',
'test_data_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/bach/test.pt',
}
lc25000_cls = {
'label_csv' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Lc25000/Lc25000_test.csv',
'train_data_dir' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Lc25000/images_224',
'test_data_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/lc25000/test.pt',
}
renalcell_cls = {
'label_csv' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Renalcell/Renalcell_test.csv',
'train_data_dir' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Renalcell/images_224',
'test_data_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/renalcell/test.pt',
}
skincancer_cls = {
'label_csv' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Skincancer/Skincancer_test.csv',
'train_data_dir' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Skincancer/images_224',
'test_data_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/skincancer/test.pt',
}
osteo_cls = {
'label_csv' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Osteo/Osteo_test.csv',
'train_data_dir' : '/ailab/group/pjlab-medai/zhouxiao/pathology/data/patch_level_data/patch_classification/Osteo/images_224',
'test_data_file' : '/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/osteo/test.pt',
}
brca_sub = {
"source":'TCGA',
"all_dir_path" : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/wsi_features/tcga/BRCA/h5_files",
"fine_dir_path" : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/wsi_features/tcga/BRCA/h5_with_label/fine",
"coarse_dir_path" : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/wsi_features/tcga/BRCA/h5_with_label/coarse",
"label_csv" : "/ailab/group/pjlab-medai/zhouxiao/pathology/features/keep/wsi_features/tcga/BRCA/tcga_brca_test.csv",
"zero_shot_template_file" : "/ailab/group/pjlab-medai/zhouxiao/pathology/prompts/subtyping/tcga_brca_prompts_all.json",
"batch_size": 4096
}