Change to folder structure on master

model_server/accessors.py → model_server/base/accessors.py

@@ -8,7 +8,7 @@ from skimage.io import imread
 import czifile
 import tifffile
 
-from model_server.process import is_mask
+from model_server.base.process import is_mask
 
 class GenericImageDataAccessor(ABC):
 

model_server/api.py → model_server/base/api.py

 from fastapi import FastAPI, HTTPException
 
-from model_server.models import DummyImageToImageModel
-from model_server.session import Session, InvalidPathError
-from model_server.validators import validate_workflow_inputs
-from model_server.workflows import infer_image_to_image
-from extensions.ilastik.workflows import infer_px_then_ob_model
+from model_server.base.models import DummyImageToImageModel
+from model_server.base.session import Session, InvalidPathError
+from model_server.base.validators import validate_workflow_inputs
+from model_server.base.workflows import infer_image_to_image
 
 app = FastAPI(debug=True)
 session = Session()
 
-import extensions.ilastik.router
-app.include_router(extensions.ilastik.router.router)
+app.include_router(model_server.extensions.ilastik.router.router)
 
 @app.on_event("startup")
 def startup():

model_server/czi_util.py → model_server/base/czi_util.py

@@ -5,7 +5,7 @@ import czifile
 import numpy as np
 import pandas as pd
 
-from model_server.accessors import InMemoryDataAccessor
+from model_server.base.accessors import InMemoryDataAccessor
 
 
 def dump_czi_subblock_table(czif: czifile.CziFile, where: Path):

model_server/models.py → model_server/base/models.py

 from abc import ABC, abstractmethod
 from math import floor
-import os
 
 import numpy as np
 
-from model_server.accessors import GenericImageDataAccessor, InMemoryDataAccessor
+from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor
 
 
 class Model(ABC):

model_server/session.py → model_server/base/session.py

@@ -5,10 +5,9 @@ from pathlib import Path
 from time import strftime, localtime
 from typing import Dict
 
-import conf.defaults
-from model_server.models import Model
-from model_server.share import SharedImageDirectory
-from model_server.workflows import WorkflowRunRecord
+import model_server.conf.defaults
+from model_server.base.models import Model
+from model_server.base.workflows import WorkflowRunRecord
 
 def create_manifest_json():
     pass
@@ -51,13 +50,13 @@ class Session(object):
         :return: dictionary of session paths
         """
         if root is None:
-            root_path = Path(conf.defaults.root)
+            root_path = Path(model_server.conf.defaults.root)
         else:
             root_path = Path(root)
         sid = Session.create_session_id(root_path)
         paths = {'root': root_path}
         for pk in ['inbound_images', 'outbound_images', 'logs']:
-            pa = root_path / sid / conf.defaults.subdirectories[pk]
+            pa = root_path / sid / model_server.conf.defaults.subdirectories[pk]
             paths[pk] = pa
             try:
                 pa.mkdir(parents=True, exist_ok=True)

model_server/util.py → model_server/base/util.py

@@ -6,8 +6,8 @@ from typing import List
 
 import pandas as pd
 
-from model_server.accessors import InMemoryDataAccessor, write_accessor_data_to_file
-from model_server.models import Model
+from model_server.base.accessors import InMemoryDataAccessor, write_accessor_data_to_file
+from model_server.base.models import Model
 
 def autonumber_new_directory(where: str, prefix: str) -> str:
     """

model_server/validators.py → model_server/base/validators.py

 from fastapi import HTTPException
 
-from model_server.session import Session
+from model_server.base.session import Session
 
 session = Session()
 

model_server/workflows.py → model_server/base/workflows.py

@@ -5,8 +5,8 @@ from pathlib import Path
 from time import perf_counter
 from typing import Dict
 
-from model_server.accessors import generate_file_accessor, write_accessor_data_to_file
-from model_server.models import Model
+from model_server.base.accessors import generate_file_accessor, write_accessor_data_to_file
+from model_server.base.models import Model
 
 from pydantic import BaseModel
 

extensions/chaeo/accessors.py → model_server/extensions/chaeo/accessors.py

@@ -2,7 +2,7 @@ from pathlib import Path
 
 import numpy as np
 
-from model_server.accessors import generate_file_accessor, InMemoryDataAccessor
+from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor
 
 class MonoPatchStack(InMemoryDataAccessor):
 

extensions/chaeo/annotators.py → model_server/extensions/chaeo/annotators.py

 import numpy as np
 from PIL import Image, ImageDraw, ImageFont
 
-from model_server.process import rescale
+from model_server.base.process import rescale
 
 def draw_boxes_on_2d_image(yx_img, boxes, **kwargs):
     pilimg = Image.fromarray(np.copy(yx_img))  # drawing modifies array in-place

extensions/chaeo/batch_jobs/20230805_kristineberg_PA.py → model_server/extensions/chaeo/batch_jobs/20230805_kristineberg_PA.py

 from pathlib import Path
 
-from model_server.util import autonumber_new_directory, get_matching_files, loop_workflow
-from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
-from extensions.ilastik.models import IlastikPixelClassifierModel
-from model_server.accessors import CziImageFileAccessor, write_accessor_data_to_file, InMemoryDataAccessor
-from model_server.process import rescale
+from model_server.base.util import autonumber_new_directory, get_matching_files, loop_workflow
+from model_server.extensions.chaeo.workflows import export_patches_from_multichannel_zstack
+from model_server.extensions.ilastik.models import IlastikPixelClassifierModel
+from model_server.base.accessors import CziImageFileAccessor, write_accessor_data_to_file, InMemoryDataAccessor
+from model_server.base.process import rescale
 
 
 def export_single_channel_tif_from_multichannel_czi(input_file_path, output_folder_path, channel, **kwargs):