Update imports (#86)

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brainglobe · Apr 16, 2020 · 83bacec · 83bacec
1 parent fb6e1c4
commit 83bacec
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Showing 6 changed files with 19 additions and 14 deletions.
diff --git a/cellfinder/__init__.py b/cellfinder/__init__.py
@@ -1,3 +1,3 @@
-__version__ = "0.3.9"
+__version__ = "0.3.10"
 __author__ = "Adam Tyson, Christian Niedworok, Charly Rousseau"
 __license__ = "GPL-3.0"
diff --git a/cellfinder/download/download.py b/cellfinder/download/download.py
@@ -5,8 +5,8 @@
 
 from imlib.general.system import disk_free_gb
 from imlib.general.config import get_config_obj
+from imlib.source import source_files
 from amap.download.download import write_atlas_to_cfg
-from cellfinder.tools import source_files
 
 
 class DownloadError(Exception):
@@ -84,8 +84,8 @@ def amend_cfg(new_atlas_folder=None, new_model_path=None, atlas=None):
     """
     print("Ensuring custom config file is correct")
 
-    original_config = source_files.source_config()
-    new_config = source_files.source_custom_config()
+    original_config = source_files.source_config_cellfinder()
+    new_config = source_files.source_custom_config_cellfinder()
     if new_atlas_folder is not None:
         write_atlas_to_cfg(
             new_atlas_folder, atlas, original_config, new_config

diff --git a/cellfinder/standard_space/cells_to_standard_space.py b/cellfinder/standard_space/cells_to_standard_space.py
@@ -14,17 +14,18 @@
 from imlib.general.system import delete_temp
 from imlib.general.exceptions import TransformationError
 from imlib.image.metadata import define_pixel_sizes
+from imlib.source.source_files import source_custom_config_cellfinder
+
 from brainio.brainio import load_any as load_any_image
 from amap.register.registration_params import RegistrationParams
 
 from cellfinder.tools import tools, prep
 import cellfinder.tools.parser as cellfinder_parse
-from cellfinder.tools.source_files import source_custom_config
 
 
 def transform_cells_to_standard_space(args):
     if args.registration_config is None:
-        args.registration_config = source_custom_config()
+        args.registration_config = source_custom_config_cellfinder()
 
     reg_params = RegistrationParams(
         args.registration_config,

diff --git a/cellfinder/tools/prep.py b/cellfinder/tools/prep.py
@@ -14,6 +14,8 @@
 from imlib.image.metadata import define_pixel_sizes
 from imlib.general.exceptions import CommandLineInputError
 from imlib.general.config import get_config_obj
+from imlib.source import source_files
+
 import amap.download.atlas as atlas_download
 
 import cellfinder.tools.tf as tf_tools
@@ -22,7 +24,7 @@
 from cellfinder.download import models as model_download
 from cellfinder.download.download import amend_cfg
 from cellfinder.download.cli import temp_dir_path
-from cellfinder.tools import tools, source_files, system
+from cellfinder.tools import tools, system
 
 
 def check_input_arg_existance(args):
@@ -412,7 +414,9 @@ def prep_registration(args, sample_name="amap"):
         amend_cfg(new_atlas_folder=atlas_dir, atlas=args.atlas)
 
     if args.registration_config is None:
-        args.registration_config = source_files.source_custom_config()
+        args.registration_config = (
+            source_files.source_custom_config_cellfinder()
+        )
     args.target_brain_path = args.background_planes_path[0]
     args.sample_name = sample_name
     logging.debug("Making registration directory")
@@ -434,7 +438,7 @@ def check_atlas_install():
     # TODO: make more sophisticated, check for all files that might be needed
     dir_exists = False
     files_exist = False
-    cfg_file_path = source_files.source_custom_config()
+    cfg_file_path = source_files.source_custom_config_cellfinder()
     if os.path.exists(cfg_file_path):
         config_obj = get_config_obj(cfg_file_path)
         atlas_conf = config_obj["atlas"]
@@ -463,7 +467,7 @@ def prep_atlas_conf(args):
             args.atlas_config = args.registration_config
         else:
             # can get atlas pixel sizes from registration config
-            args.atlas_config = source_files.source_custom_config()
+            args.atlas_config = source_files.source_custom_config_cellfinder()
     return args
 
 
@@ -491,7 +495,7 @@ def prep_models(args):
     if args.trained_model is None and args.model_weights is None:
         logging.debug("No model or weights supplied, so using the default")
 
-        config_file = source_files.source_custom_config()
+        config_file = source_files.source_custom_config_cellfinder()
         if not Path(config_file).exists():
             logging.debug("Custom config does not exist, downloading models")
             model_path = model_download.main(args.model, args.install_path)

diff --git a/cellfinder/utils/roi_transform.py b/cellfinder/utils/roi_transform.py
@@ -22,7 +22,7 @@
     SafeExecuteCommandError,
 )
 from imlib.general.exceptions import RegistrationError
-from cellfinder.tools.source_files import source_custom_config
+from imlib.source.source_files import source_custom_config_cellfinder
 from amap.config.atlas import Atlas
 from amap.config.config import get_binary
 from amap.tools.source_files import get_niftyreg_binaries
@@ -278,7 +278,7 @@ def main():
     print(f"ROI file is: {rois}")
 
     if args.registration_config is None:
-        args.registration_config = source_custom_config()
+        args.registration_config = source_custom_config_cellfinder()
     atlas = Atlas(args.registration_config)
     source_image = args.reg_dir / SOURCE_IMAGE_NAME
     print(f"Source image is: {source_image}")

diff --git a/setup.py b/setup.py
@@ -93,7 +93,7 @@
 
 setup(
     name="cellfinder",
-    version="0.3.9",
+    version="0.3.10",
     description="Automated 3D cell detection and registration of whole-brain images",
     long_description=long_description,
     long_description_content_type="text/markdown",