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Fix relative imports #304

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merged 1 commit into from
Sep 12, 2023
Merged

Fix relative imports #304

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8 changes: 3 additions & 5 deletions em_workflows/brt/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,8 +50,8 @@
from em_workflows.utils import neuroglancer as ng
from em_workflows.constants import AssetType

from .config import BRTConfig
from .constants import BRT_DEPTH, BRT_HEIGHT, BRT_WIDTH
from em_workflows.brt.config import BRTConfig
from em_workflows.brt.constants import BRT_DEPTH, BRT_HEIGHT, BRT_WIDTH

"""
Batchruntomo pipeline overview:
Expand Down Expand Up @@ -397,9 +397,7 @@ def gen_ave_8_vol(file_path: FilePath) -> dict:
log_file = f"{file_path.working_dir}/ave_8_mrc.log"
FilePath.run(cmd=cmd, log_file=log_file)
asset_fp = file_path.copy_to_assets_dir(fp_to_cp=Path(ave_8_mrc))
bin_vol_asset = file_path.gen_asset(
asset_type=AssetType.VOLUME, asset_fp=asset_fp
)
bin_vol_asset = file_path.gen_asset(asset_type=AssetType.VOLUME, asset_fp=asset_fp)
return bin_vol_asset


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4 changes: 2 additions & 2 deletions em_workflows/czi/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,15 @@
from em_workflows.file_path import FilePath
from em_workflows.utils import utils
from prefect.run_configs import LocalRun
from .constants import (
from em_workflows.czi.constants import (
BIOFORMATS_NUM_WORKERS,
RECHUNK_SIZE,
VALID_CZI_INPUTS,
THUMB_X_DIM,
THUMB_Y_DUM,
SITK_COMPRESSION_LVL,
)
from .config import CZIConfig
from em_workflows.czi.config import CZIConfig


def rechunk_zarr(zarr_fp: Path) -> None:
Expand Down
4 changes: 2 additions & 2 deletions em_workflows/dm_conversion/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
from em_workflows.utils import utils
from em_workflows.file_path import FilePath
from em_workflows.constants import LARGE_DIM, AssetType
from .config import DMConfig
from .constants import LARGE_2D, SMALL_2D, VALID_2D_INPUT_EXTS
from em_workflows.dm_conversion.config import DMConfig
from em_workflows.dm_conversion.constants import LARGE_2D, SMALL_2D, VALID_2D_INPUT_EXTS


@task
Expand Down
4 changes: 2 additions & 2 deletions em_workflows/lrg_2d_rgb/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@
from em_workflows.utils import utils
from em_workflows.file_path import FilePath
from em_workflows.constants import AssetType
from .config import LRG2DConfig
from .constants import (
from em_workflows.lrg_2d_rgb.config import LRG2DConfig
from em_workflows.lrg_2d_rgb.constants import (
LARGE_THUMB_X,
LARGE_THUMB_Y,
SMALL_THUMB_X,
Expand Down
12 changes: 4 additions & 8 deletions em_workflows/sem_tomo/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
from em_workflows.utils import utils
from em_workflows.utils import neuroglancer as ng
from em_workflows.constants import AssetType
from .config import SEMConfig
from .constants import FIBSEM_DEPTH, FIBSEM_HEIGHT, FIBSEM_WIDTH
from em_workflows.sem_tomo.config import SEMConfig
from em_workflows.sem_tomo.constants import FIBSEM_DEPTH, FIBSEM_HEIGHT, FIBSEM_WIDTH


@task
Expand Down Expand Up @@ -174,9 +174,7 @@ def gen_keyimg(fp_in: FilePath) -> Dict:
utils.log(f"Created keyimg {cmd}")
FilePath.run(cmd=cmd, log_file=log_file)
asset_fp = fp_in.copy_to_assets_dir(fp_to_cp=keyimg_fp)
keyimg_asset = fp_in.gen_asset(
asset_type=AssetType.KEY_IMAGE, asset_fp=asset_fp
)
keyimg_asset = fp_in.gen_asset(asset_type=AssetType.KEY_IMAGE, asset_fp=asset_fp)
return keyimg_asset


Expand Down Expand Up @@ -205,9 +203,7 @@ def gen_keyimg_small(fp_in: FilePath) -> Dict:
utils.log(f"Created {cmd}")
FilePath.run(cmd=cmd, log_file=log_file)
asset_fp = fp_in.copy_to_assets_dir(fp_to_cp=keyimg_sm_fp)
keyimg_asset = fp_in.gen_asset(
asset_type=AssetType.THUMBNAIL, asset_fp=asset_fp
)
keyimg_asset = fp_in.gen_asset(asset_type=AssetType.THUMBNAIL, asset_fp=asset_fp)
return keyimg_asset


Expand Down
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