From 33f043947545d439c6bf1f0533d53c5ef9d1ecc6 Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Wed, 5 Feb 2020 14:39:07 +0100
Subject: [PATCH] Rename python module from scripts to mmpb
---
analysis/cell_volumes.py | 4 ++--
analysis/correct_intensities.py | 2 +-
analysis/extend_regions/recompute_table.py | 6 +++---
analysis/ganglia/write_ganglion_segmentation.py | 4 ++--
analysis/gene_expression.py | 4 ++--
analysis/nephridia/morphology.py | 3 +--
extract_from_platybrowser.py | 2 +-
make_dev_folder.py | 2 +-
{scripts => mmpb}/__init__.py | 0
{scripts => mmpb}/analysis/__init__.py | 0
{scripts => mmpb}/analysis/counts.py | 0
{scripts => mmpb}/analysis/expression.py | 0
{scripts => mmpb}/analysis/morphology.py | 0
{scripts => mmpb}/analysis/nephridia.py | 0
{scripts => mmpb}/attributes/__init__.py | 0
{scripts => mmpb}/attributes/base_attributes.py | 0
.../attributes/cell_nucleus_mapping.py | 0
{scripts => mmpb}/attributes/cilia_attributes.py | 0
{scripts => mmpb}/attributes/genes.py | 0
{scripts => mmpb}/attributes/master.py | 0
{scripts => mmpb}/attributes/morphology.py | 0
.../attributes/region_attributes.py | 0
{scripts => mmpb}/attributes/util.py | 0
{scripts => mmpb}/bookmarks.py | 0
{scripts => mmpb}/check_attributes.py | 0
{scripts => mmpb}/default_config.py | 0
{scripts => mmpb}/export/__init__.py | 0
{scripts => mmpb}/export/export_segmentation.py | 0
.../export/extract_neuron_traces.py | 0
{scripts => mmpb}/export/extract_subvolume.py | 0
{scripts => mmpb}/export/map_segmentation_ids.py | 0
{scripts => mmpb}/export/to_bdv.py | 0
{scripts => mmpb}/extension/__init__.py | 0
.../extension/attributes/__init__.py | 0
{scripts => mmpb}/extension/attributes/genes.py | 2 +-
.../extension/attributes/genes_impl.py | 0
.../extension/attributes/morphology.py | 4 ++--
.../extension/attributes/morphology_impl.py | 0
.../extension/attributes/vc_assignments.py | 2 +-
.../extension/attributes/vc_assignments_impl.py | 0
.../extension/attributes/workflow.py | 0
.../extension/registration/__init__.py | 0
.../extension/registration/apply_registration.py | 0
.../segmentation/nucleus_assignments/__init__.py | 0
.../nucleus_assignments/map_nuclei.py | 0
.../nucleus_assignment_workflow.py | 0
.../extension/segmentation/unmerge/__init__.py | 0
.../segmentation/unmerge/find_merges.py | 0
.../extension/segmentation/unmerge/fix_merges.py | 0
.../segmentation/unmerge/unmerge_workflow.py | 0
{scripts => mmpb}/files/__init__.py | 0
{scripts => mmpb}/files/bdv_server.py | 0
{scripts => mmpb}/files/checks.py | 0
{scripts => mmpb}/files/copy_helper.py | 0
{scripts => mmpb}/files/folders.py | 0
{scripts => mmpb}/files/for_upload.py | 2 +-
{scripts => mmpb}/files/sources.py | 2 +-
{scripts => mmpb}/files/xml_utils.py | 0
{scripts => mmpb}/release_helper.py | 0
{scripts => mmpb}/segmentation/__init__.py | 0
{scripts => mmpb}/segmentation/cells/__init__.py | 0
.../segmentation/cells/multicut/__init__.py | 0
.../cells/multicut/segmentation_workflow.py | 6 +++---
{scripts => mmpb}/segmentation/cilia/__init__.py | 0
.../segmentation/correction/__init__.py | 0
.../segmentation/correction/annotation_tool.py | 0
.../segmentation/correction/assignment_diffs.py | 0
.../correction/cillia_correction_tool.py | 2 +-
.../segmentation/correction/correction_tool.py | 0
.../correction/export_node_labels.py | 0
.../segmentation/correction/heuristics.py | 0
.../segmentation/correction/preprocess.py | 0
.../segmentation/cuticle/__init__.py | 0
.../segmentation/muscle/__init__.py | 0
.../segmentation/muscle/muscle_mapping.py | 0
.../segmentation/muscle/workflow.py | 0
.../segmentation/nuclei/__init__.py | 0
.../segmentation/tissue/__init__.py | 0
.../segmentation/validation/__init__.py | 0
.../segmentation/validation/eval_cells.py | 0
.../segmentation/validation/eval_nuclei.py | 0
.../validation/evaluate_annotations.py | 0
.../validation/refine_annotations.py | 0
{scripts => mmpb}/transformation/__init__.py | 0
.../transformation/intensity_correction.py | 0
{scripts => mmpb}/util.py | 0
registration/apply_registration.py | 2 +-
segmentation/cell_segmentation.py | 2 +-
segmentation/compute_default_table.py | 2 +-
.../correction/correct_cell_segmentation.py | 16 ++++++++--------
segmentation/correction/deprecated.py | 2 +-
segmentation/correction/fix_assignments.py | 4 ++--
segmentation/correction/morphology_outlier.py | 8 ++++----
segmentation/muscles.py | 4 ++--
segmentation/neuron_traces.py | 2 +-
segmentation/validation/check_validation.py | 10 +++++-----
.../validation/eval_cell_segmentation.py | 6 +++---
.../validation/eval_nucleus_segmentation.py | 2 +-
segmentation/validation/proofread_annotations.py | 4 ++--
test/attributes/test_base.py | 2 +-
test/attributes/test_cell_nucleus_mapping.py | 2 +-
test/attributes/test_cilia.py | 2 +-
test/attributes/test_genes.py | 6 +++---
test/attributes/test_morphology.py | 10 +++++-----
test/attributes/test_regions.py | 2 +-
test/cilia.py | 3 +--
test/registration/test_wrapper.py | 2 +-
update_major.py | 4 ++--
update_minor.py | 4 ++--
update_patch.py | 14 +++++++-------
update_registration.py | 16 ++++++++--------
111 files changed, 88 insertions(+), 90 deletions(-)
rename {scripts => mmpb}/__init__.py (100%)
rename {scripts => mmpb}/analysis/__init__.py (100%)
rename {scripts => mmpb}/analysis/counts.py (100%)
rename {scripts => mmpb}/analysis/expression.py (100%)
rename {scripts => mmpb}/analysis/morphology.py (100%)
rename {scripts => mmpb}/analysis/nephridia.py (100%)
rename {scripts => mmpb}/attributes/__init__.py (100%)
rename {scripts => mmpb}/attributes/base_attributes.py (100%)
rename {scripts => mmpb}/attributes/cell_nucleus_mapping.py (100%)
rename {scripts => mmpb}/attributes/cilia_attributes.py (100%)
rename {scripts => mmpb}/attributes/genes.py (100%)
rename {scripts => mmpb}/attributes/master.py (100%)
rename {scripts => mmpb}/attributes/morphology.py (100%)
rename {scripts => mmpb}/attributes/region_attributes.py (100%)
rename {scripts => mmpb}/attributes/util.py (100%)
rename {scripts => mmpb}/bookmarks.py (100%)
rename {scripts => mmpb}/check_attributes.py (100%)
rename {scripts => mmpb}/default_config.py (100%)
rename {scripts => mmpb}/export/__init__.py (100%)
rename {scripts => mmpb}/export/export_segmentation.py (100%)
rename {scripts => mmpb}/export/extract_neuron_traces.py (100%)
rename {scripts => mmpb}/export/extract_subvolume.py (100%)
rename {scripts => mmpb}/export/map_segmentation_ids.py (100%)
rename {scripts => mmpb}/export/to_bdv.py (100%)
rename {scripts => mmpb}/extension/__init__.py (100%)
rename {scripts => mmpb}/extension/attributes/__init__.py (100%)
rename {scripts => mmpb}/extension/attributes/genes.py (97%)
rename {scripts => mmpb}/extension/attributes/genes_impl.py (100%)
rename {scripts => mmpb}/extension/attributes/morphology.py (98%)
rename {scripts => mmpb}/extension/attributes/morphology_impl.py (100%)
rename {scripts => mmpb}/extension/attributes/vc_assignments.py (96%)
rename {scripts => mmpb}/extension/attributes/vc_assignments_impl.py (100%)
rename {scripts => mmpb}/extension/attributes/workflow.py (100%)
rename {scripts => mmpb}/extension/registration/__init__.py (100%)
rename {scripts => mmpb}/extension/registration/apply_registration.py (100%)
rename {scripts => mmpb}/extension/segmentation/nucleus_assignments/__init__.py (100%)
rename {scripts => mmpb}/extension/segmentation/nucleus_assignments/map_nuclei.py (100%)
rename {scripts => mmpb}/extension/segmentation/nucleus_assignments/nucleus_assignment_workflow.py (100%)
rename {scripts => mmpb}/extension/segmentation/unmerge/__init__.py (100%)
rename {scripts => mmpb}/extension/segmentation/unmerge/find_merges.py (100%)
rename {scripts => mmpb}/extension/segmentation/unmerge/fix_merges.py (100%)
rename {scripts => mmpb}/extension/segmentation/unmerge/unmerge_workflow.py (100%)
rename {scripts => mmpb}/files/__init__.py (100%)
rename {scripts => mmpb}/files/bdv_server.py (100%)
rename {scripts => mmpb}/files/checks.py (100%)
rename {scripts => mmpb}/files/copy_helper.py (100%)
rename {scripts => mmpb}/files/folders.py (100%)
rename {scripts => mmpb}/files/for_upload.py (99%)
rename {scripts => mmpb}/files/sources.py (99%)
rename {scripts => mmpb}/files/xml_utils.py (100%)
rename {scripts => mmpb}/release_helper.py (100%)
rename {scripts => mmpb}/segmentation/__init__.py (100%)
rename {scripts => mmpb}/segmentation/cells/__init__.py (100%)
rename {scripts => mmpb}/segmentation/cells/multicut/__init__.py (100%)
rename {scripts => mmpb}/segmentation/cells/multicut/segmentation_workflow.py (98%)
rename {scripts => mmpb}/segmentation/cilia/__init__.py (100%)
rename {scripts => mmpb}/segmentation/correction/__init__.py (100%)
rename {scripts => mmpb}/segmentation/correction/annotation_tool.py (100%)
rename {scripts => mmpb}/segmentation/correction/assignment_diffs.py (100%)
rename {scripts => mmpb}/segmentation/correction/cillia_correction_tool.py (99%)
rename {scripts => mmpb}/segmentation/correction/correction_tool.py (100%)
rename {scripts => mmpb}/segmentation/correction/export_node_labels.py (100%)
rename {scripts => mmpb}/segmentation/correction/heuristics.py (100%)
rename {scripts => mmpb}/segmentation/correction/preprocess.py (100%)
rename {scripts => mmpb}/segmentation/cuticle/__init__.py (100%)
rename {scripts => mmpb}/segmentation/muscle/__init__.py (100%)
rename {scripts => mmpb}/segmentation/muscle/muscle_mapping.py (100%)
rename {scripts => mmpb}/segmentation/muscle/workflow.py (100%)
rename {scripts => mmpb}/segmentation/nuclei/__init__.py (100%)
rename {scripts => mmpb}/segmentation/tissue/__init__.py (100%)
rename {scripts => mmpb}/segmentation/validation/__init__.py (100%)
rename {scripts => mmpb}/segmentation/validation/eval_cells.py (100%)
rename {scripts => mmpb}/segmentation/validation/eval_nuclei.py (100%)
rename {scripts => mmpb}/segmentation/validation/evaluate_annotations.py (100%)
rename {scripts => mmpb}/segmentation/validation/refine_annotations.py (100%)
rename {scripts => mmpb}/transformation/__init__.py (100%)
rename {scripts => mmpb}/transformation/intensity_correction.py (100%)
rename {scripts => mmpb}/util.py (100%)
diff --git a/analysis/cell_volumes.py b/analysis/cell_volumes.py
index 7bebba5..2427d99 100644
--- a/analysis/cell_volumes.py
+++ b/analysis/cell_volumes.py
@@ -3,8 +3,8 @@
import argparse
import os
import numpy as np
-from scripts import get_latest_version
-from scripts.analysis import get_region_ids, get_morphology_attribute
+from mmpb import get_latest_version
+from mmpb.analysis import get_region_ids, get_morphology_attribute
def cell_volumes(region_name, version):
diff --git a/analysis/correct_intensities.py b/analysis/correct_intensities.py
index 253b853..58853c8 100644
--- a/analysis/correct_intensities.py
+++ b/analysis/correct_intensities.py
@@ -10,7 +10,7 @@ import luigi
import vigra
from scipy.ndimage.morphology import binary_dilation
-from scripts.transformation import intensity_correction
+from mmpb.transformation import intensity_correction
from pybdv import make_bdv
from pybdv.metadata import write_h5_metadata
diff --git a/analysis/extend_regions/recompute_table.py b/analysis/extend_regions/recompute_table.py
index 089c7da..e601239 100644
--- a/analysis/extend_regions/recompute_table.py
+++ b/analysis/extend_regions/recompute_table.py
@@ -2,9 +2,9 @@ import os
import h5py
import numpy as np
-from scripts.default_config import write_default_global_config
-from scripts.attributes.region_attributes import region_attributes
-from scripts.files.xml_utils import get_h5_path_from_xml
+from mmpb.default_config import write_default_global_config
+from mmpb.attributes.region_attributes import region_attributes
+from mmpb.files.xml_utils import get_h5_path_from_xml
def recompute_table(version):
diff --git a/analysis/ganglia/write_ganglion_segmentation.py b/analysis/ganglia/write_ganglion_segmentation.py
index 4c0ecbc..523313a 100644
--- a/analysis/ganglia/write_ganglion_segmentation.py
+++ b/analysis/ganglia/write_ganglion_segmentation.py
@@ -5,7 +5,7 @@ import numpy as np
import pandas as pd
import nifty.tools as nt
from pybdv import make_bdv
-from scripts.attributes.base_attributes import base_attributes
+from mmpb.attributes.base_attributes import base_attributes
# Segmentation version: 0.2.1
@@ -64,7 +64,7 @@ def make_table():
def make_overlap_table():
- from scripts.attributes.util import write_csv, node_labels
+ from mmpb.attributes.util import write_csv, node_labels
tmp_folder = './tmp_ganglia'
target = 'slurm'
max_jobs = 200
diff --git a/analysis/gene_expression.py b/analysis/gene_expression.py
index 3c83413..0d1bbd7 100644
--- a/analysis/gene_expression.py
+++ b/analysis/gene_expression.py
@@ -3,8 +3,8 @@ import argparse
import os
import json
import numpy as np
-from scripts import get_latest_version
-from scripts.analysis import get_cells_expressing_genes
+from mmpb import get_latest_version
+from mmpb.analysis import get_cells_expressing_genes
def count_gene_expression(gene_names, threshold, version, query):
diff --git a/analysis/nephridia/morphology.py b/analysis/nephridia/morphology.py
index 36426ce..726e811 100644
--- a/analysis/nephridia/morphology.py
+++ b/analysis/nephridia/morphology.py
@@ -1,8 +1,7 @@
import os
import numpy as np
import pandas as pd
-from scripts.analysis.nephridia import filter_by_size, plot_sizes
-from scripts.analysis.nephridia import match_cilia_to_cells
+from mmpb.analysis.nephridia import filter_by_size, match_cilia_to_cells
cell_ids = [24449, 22584, 21904, 21590, 21594, 21595, 21910, 21911, 21915]
print("Number of cells:", len(cell_ids))
diff --git a/extract_from_platybrowser.py b/extract_from_platybrowser.py
index ea5a04f..db855d2 100755
--- a/extract_from_platybrowser.py
+++ b/extract_from_platybrowser.py
@@ -3,7 +3,7 @@
import argparse
import os
import pandas as pd
-from scripts.export.extract_subvolume import make_cutout, get_res_level, parse_coordinate, name_to_path
+from mmpb.export.extract_subvolume import make_cutout, get_res_level, parse_coordinate, name_to_path
def get_bounding_box(tag, lower, upper, table_name, table_id):
diff --git a/make_dev_folder.py b/make_dev_folder.py
index 56504e2..60d188f 100644
--- a/make_dev_folder.py
+++ b/make_dev_folder.py
@@ -3,7 +3,7 @@
import argparse
import os
from subprocess import check_output
-from scripts.files import copy_release_folder, make_folder_structure
+from mmpb.files import copy_release_folder, make_folder_structure
def make_dev_folder(dev_name, version=''):
diff --git a/scripts/__init__.py b/mmpb/__init__.py
similarity index 100%
rename from scripts/__init__.py
rename to mmpb/__init__.py
diff --git a/scripts/analysis/__init__.py b/mmpb/analysis/__init__.py
similarity index 100%
rename from scripts/analysis/__init__.py
rename to mmpb/analysis/__init__.py
diff --git a/scripts/analysis/counts.py b/mmpb/analysis/counts.py
similarity index 100%
rename from scripts/analysis/counts.py
rename to mmpb/analysis/counts.py
diff --git a/scripts/analysis/expression.py b/mmpb/analysis/expression.py
similarity index 100%
rename from scripts/analysis/expression.py
rename to mmpb/analysis/expression.py
diff --git a/scripts/analysis/morphology.py b/mmpb/analysis/morphology.py
similarity index 100%
rename from scripts/analysis/morphology.py
rename to mmpb/analysis/morphology.py
diff --git a/scripts/analysis/nephridia.py b/mmpb/analysis/nephridia.py
similarity index 100%
rename from scripts/analysis/nephridia.py
rename to mmpb/analysis/nephridia.py
diff --git a/scripts/attributes/__init__.py b/mmpb/attributes/__init__.py
similarity index 100%
rename from scripts/attributes/__init__.py
rename to mmpb/attributes/__init__.py
diff --git a/scripts/attributes/base_attributes.py b/mmpb/attributes/base_attributes.py
similarity index 100%
rename from scripts/attributes/base_attributes.py
rename to mmpb/attributes/base_attributes.py
diff --git a/scripts/attributes/cell_nucleus_mapping.py b/mmpb/attributes/cell_nucleus_mapping.py
similarity index 100%
rename from scripts/attributes/cell_nucleus_mapping.py
rename to mmpb/attributes/cell_nucleus_mapping.py
diff --git a/scripts/attributes/cilia_attributes.py b/mmpb/attributes/cilia_attributes.py
similarity index 100%
rename from scripts/attributes/cilia_attributes.py
rename to mmpb/attributes/cilia_attributes.py
diff --git a/scripts/attributes/genes.py b/mmpb/attributes/genes.py
similarity index 100%
rename from scripts/attributes/genes.py
rename to mmpb/attributes/genes.py
diff --git a/scripts/attributes/master.py b/mmpb/attributes/master.py
similarity index 100%
rename from scripts/attributes/master.py
rename to mmpb/attributes/master.py
diff --git a/scripts/attributes/morphology.py b/mmpb/attributes/morphology.py
similarity index 100%
rename from scripts/attributes/morphology.py
rename to mmpb/attributes/morphology.py
diff --git a/scripts/attributes/region_attributes.py b/mmpb/attributes/region_attributes.py
similarity index 100%
rename from scripts/attributes/region_attributes.py
rename to mmpb/attributes/region_attributes.py
diff --git a/scripts/attributes/util.py b/mmpb/attributes/util.py
similarity index 100%
rename from scripts/attributes/util.py
rename to mmpb/attributes/util.py
diff --git a/scripts/bookmarks.py b/mmpb/bookmarks.py
similarity index 100%
rename from scripts/bookmarks.py
rename to mmpb/bookmarks.py
diff --git a/scripts/check_attributes.py b/mmpb/check_attributes.py
similarity index 100%
rename from scripts/check_attributes.py
rename to mmpb/check_attributes.py
diff --git a/scripts/default_config.py b/mmpb/default_config.py
similarity index 100%
rename from scripts/default_config.py
rename to mmpb/default_config.py
diff --git a/scripts/export/__init__.py b/mmpb/export/__init__.py
similarity index 100%
rename from scripts/export/__init__.py
rename to mmpb/export/__init__.py
diff --git a/scripts/export/export_segmentation.py b/mmpb/export/export_segmentation.py
similarity index 100%
rename from scripts/export/export_segmentation.py
rename to mmpb/export/export_segmentation.py
diff --git a/scripts/export/extract_neuron_traces.py b/mmpb/export/extract_neuron_traces.py
similarity index 100%
rename from scripts/export/extract_neuron_traces.py
rename to mmpb/export/extract_neuron_traces.py
diff --git a/scripts/export/extract_subvolume.py b/mmpb/export/extract_subvolume.py
similarity index 100%
rename from scripts/export/extract_subvolume.py
rename to mmpb/export/extract_subvolume.py
diff --git a/scripts/export/map_segmentation_ids.py b/mmpb/export/map_segmentation_ids.py
similarity index 100%
rename from scripts/export/map_segmentation_ids.py
rename to mmpb/export/map_segmentation_ids.py
diff --git a/scripts/export/to_bdv.py b/mmpb/export/to_bdv.py
similarity index 100%
rename from scripts/export/to_bdv.py
rename to mmpb/export/to_bdv.py
diff --git a/scripts/extension/__init__.py b/mmpb/extension/__init__.py
similarity index 100%
rename from scripts/extension/__init__.py
rename to mmpb/extension/__init__.py
diff --git a/scripts/extension/attributes/__init__.py b/mmpb/extension/attributes/__init__.py
similarity index 100%
rename from scripts/extension/attributes/__init__.py
rename to mmpb/extension/attributes/__init__.py
diff --git a/scripts/extension/attributes/genes.py b/mmpb/extension/attributes/genes.py
similarity index 97%
rename from scripts/extension/attributes/genes.py
rename to mmpb/extension/attributes/genes.py
index 8094c6e..841363a 100644
--- a/scripts/extension/attributes/genes.py
+++ b/mmpb/extension/attributes/genes.py
@@ -10,7 +10,7 @@ import numpy as np
import cluster_tools.utils.function_utils as fu
from cluster_tools.utils.task_utils import DummyTask
from cluster_tools.cluster_tasks import SlurmTask, LocalTask
-from scripts.extension.attributes.genes_impl import gene_assignments
+from mmpb.extension.attributes.genes_impl import gene_assignments
#
# Gene Attribute Tasks
diff --git a/scripts/extension/attributes/genes_impl.py b/mmpb/extension/attributes/genes_impl.py
similarity index 100%
rename from scripts/extension/attributes/genes_impl.py
rename to mmpb/extension/attributes/genes_impl.py
diff --git a/scripts/extension/attributes/morphology.py b/mmpb/extension/attributes/morphology.py
similarity index 98%
rename from scripts/extension/attributes/morphology.py
rename to mmpb/extension/attributes/morphology.py
index 80f1cbb..24d9893 100644
--- a/scripts/extension/attributes/morphology.py
+++ b/mmpb/extension/attributes/morphology.py
@@ -13,8 +13,8 @@ import cluster_tools.utils.volume_utils as vu
import cluster_tools.utils.function_utils as fu
from cluster_tools.utils.task_utils import DummyTask
from cluster_tools.cluster_tasks import SlurmTask, LocalTask
-from scripts.extension.attributes.morphology_impl import (morphology_impl_cell,
- morphology_impl_nucleus)
+from mmpb.extension.attributes.morphology_impl import (morphology_impl_cell,
+ morphology_impl_nucleus)
#
# Morphology Attribute Tasks
diff --git a/scripts/extension/attributes/morphology_impl.py b/mmpb/extension/attributes/morphology_impl.py
similarity index 100%
rename from scripts/extension/attributes/morphology_impl.py
rename to mmpb/extension/attributes/morphology_impl.py
diff --git a/scripts/extension/attributes/vc_assignments.py b/mmpb/extension/attributes/vc_assignments.py
similarity index 96%
rename from scripts/extension/attributes/vc_assignments.py
rename to mmpb/extension/attributes/vc_assignments.py
index 5b604b8..b1690a1 100644
--- a/scripts/extension/attributes/vc_assignments.py
+++ b/mmpb/extension/attributes/vc_assignments.py
@@ -9,7 +9,7 @@ import luigi
import cluster_tools.utils.function_utils as fu
from cluster_tools.utils.task_utils import DummyTask
from cluster_tools.cluster_tasks import SlurmTask, LocalTask
-from scripts.extension.attributes.vc_assignments_impl import vc_assignments as vc_assignments_impl
+from mmpb.extension.attributes.vc_assignments_impl import vc_assignments as vc_assignments_impl
#
# Gene Attribute Tasks
diff --git a/scripts/extension/attributes/vc_assignments_impl.py b/mmpb/extension/attributes/vc_assignments_impl.py
similarity index 100%
rename from scripts/extension/attributes/vc_assignments_impl.py
rename to mmpb/extension/attributes/vc_assignments_impl.py
diff --git a/scripts/extension/attributes/workflow.py b/mmpb/extension/attributes/workflow.py
similarity index 100%
rename from scripts/extension/attributes/workflow.py
rename to mmpb/extension/attributes/workflow.py
diff --git a/scripts/extension/registration/__init__.py b/mmpb/extension/registration/__init__.py
similarity index 100%
rename from scripts/extension/registration/__init__.py
rename to mmpb/extension/registration/__init__.py
diff --git a/scripts/extension/registration/apply_registration.py b/mmpb/extension/registration/apply_registration.py
similarity index 100%
rename from scripts/extension/registration/apply_registration.py
rename to mmpb/extension/registration/apply_registration.py
diff --git a/scripts/extension/segmentation/nucleus_assignments/__init__.py b/mmpb/extension/segmentation/nucleus_assignments/__init__.py
similarity index 100%
rename from scripts/extension/segmentation/nucleus_assignments/__init__.py
rename to mmpb/extension/segmentation/nucleus_assignments/__init__.py
diff --git a/scripts/extension/segmentation/nucleus_assignments/map_nuclei.py b/mmpb/extension/segmentation/nucleus_assignments/map_nuclei.py
similarity index 100%
rename from scripts/extension/segmentation/nucleus_assignments/map_nuclei.py
rename to mmpb/extension/segmentation/nucleus_assignments/map_nuclei.py
diff --git a/scripts/extension/segmentation/nucleus_assignments/nucleus_assignment_workflow.py b/mmpb/extension/segmentation/nucleus_assignments/nucleus_assignment_workflow.py
similarity index 100%
rename from scripts/extension/segmentation/nucleus_assignments/nucleus_assignment_workflow.py
rename to mmpb/extension/segmentation/nucleus_assignments/nucleus_assignment_workflow.py
diff --git a/scripts/extension/segmentation/unmerge/__init__.py b/mmpb/extension/segmentation/unmerge/__init__.py
similarity index 100%
rename from scripts/extension/segmentation/unmerge/__init__.py
rename to mmpb/extension/segmentation/unmerge/__init__.py
diff --git a/scripts/extension/segmentation/unmerge/find_merges.py b/mmpb/extension/segmentation/unmerge/find_merges.py
similarity index 100%
rename from scripts/extension/segmentation/unmerge/find_merges.py
rename to mmpb/extension/segmentation/unmerge/find_merges.py
diff --git a/scripts/extension/segmentation/unmerge/fix_merges.py b/mmpb/extension/segmentation/unmerge/fix_merges.py
similarity index 100%
rename from scripts/extension/segmentation/unmerge/fix_merges.py
rename to mmpb/extension/segmentation/unmerge/fix_merges.py
diff --git a/scripts/extension/segmentation/unmerge/unmerge_workflow.py b/mmpb/extension/segmentation/unmerge/unmerge_workflow.py
similarity index 100%
rename from scripts/extension/segmentation/unmerge/unmerge_workflow.py
rename to mmpb/extension/segmentation/unmerge/unmerge_workflow.py
diff --git a/scripts/files/__init__.py b/mmpb/files/__init__.py
similarity index 100%
rename from scripts/files/__init__.py
rename to mmpb/files/__init__.py
diff --git a/scripts/files/bdv_server.py b/mmpb/files/bdv_server.py
similarity index 100%
rename from scripts/files/bdv_server.py
rename to mmpb/files/bdv_server.py
diff --git a/scripts/files/checks.py b/mmpb/files/checks.py
similarity index 100%
rename from scripts/files/checks.py
rename to mmpb/files/checks.py
diff --git a/scripts/files/copy_helper.py b/mmpb/files/copy_helper.py
similarity index 100%
rename from scripts/files/copy_helper.py
rename to mmpb/files/copy_helper.py
diff --git a/scripts/files/folders.py b/mmpb/files/folders.py
similarity index 100%
rename from scripts/files/folders.py
rename to mmpb/files/folders.py
diff --git a/scripts/files/for_upload.py b/mmpb/files/for_upload.py
similarity index 99%
rename from scripts/files/for_upload.py
rename to mmpb/files/for_upload.py
index 0e38ea5..d944193 100644
--- a/scripts/files/for_upload.py
+++ b/mmpb/files/for_upload.py
@@ -3,7 +3,7 @@ import xml.etree.ElementTree as ET
import numpy as np
from shutil import copyfile
-from scripts.files.xml_utils import get_h5_path_from_xml
+from mmpb.files.xml_utils import get_h5_path_from_xml
from glob import glob
from elf.io import open_file
from pybdv.converter import copy_dataset
diff --git a/scripts/files/sources.py b/mmpb/files/sources.py
similarity index 99%
rename from scripts/files/sources.py
rename to mmpb/files/sources.py
index 17c3266..6ff3f7e 100644
--- a/scripts/files/sources.py
+++ b/mmpb/files/sources.py
@@ -176,7 +176,7 @@ def add_segmentation(source_name, name, segmentation_path=None,
Adding a dynamic segmentation:
```
- # 'update_seg_table' must be importable from 'scripts.attributes'
+ # 'update_seg_table' must be importable from 'mmpb.attributes'
add_segmentation(source_name, seg_name,
paintera_project=('/path/to/paintera/root.n5', '/path/in/file'),
resolution=(.025, .02, .02), # resolution in microns, must be passed for dynamic seg
diff --git a/scripts/files/xml_utils.py b/mmpb/files/xml_utils.py
similarity index 100%
rename from scripts/files/xml_utils.py
rename to mmpb/files/xml_utils.py
diff --git a/scripts/release_helper.py b/mmpb/release_helper.py
similarity index 100%
rename from scripts/release_helper.py
rename to mmpb/release_helper.py
diff --git a/scripts/segmentation/__init__.py b/mmpb/segmentation/__init__.py
similarity index 100%
rename from scripts/segmentation/__init__.py
rename to mmpb/segmentation/__init__.py
diff --git a/scripts/segmentation/cells/__init__.py b/mmpb/segmentation/cells/__init__.py
similarity index 100%
rename from scripts/segmentation/cells/__init__.py
rename to mmpb/segmentation/cells/__init__.py
diff --git a/scripts/segmentation/cells/multicut/__init__.py b/mmpb/segmentation/cells/multicut/__init__.py
similarity index 100%
rename from scripts/segmentation/cells/multicut/__init__.py
rename to mmpb/segmentation/cells/multicut/__init__.py
diff --git a/scripts/segmentation/cells/multicut/segmentation_workflow.py b/mmpb/segmentation/cells/multicut/segmentation_workflow.py
similarity index 98%
rename from scripts/segmentation/cells/multicut/segmentation_workflow.py
rename to mmpb/segmentation/cells/multicut/segmentation_workflow.py
index 62bfb27..b580cbd 100644
--- a/scripts/segmentation/cells/multicut/segmentation_workflow.py
+++ b/mmpb/segmentation/cells/multicut/segmentation_workflow.py
@@ -8,10 +8,10 @@ from cluster_tools.affinities import InsertAffinitiesWorkflow
from cluster_tools.morphology import MorphologyWorkflow
from cluster_tools.postprocess import SizeFilterAndGraphWatershedWorkflow
-from scripts.default_config import write_default_global_config
+from mmpb.default_config import write_default_global_config
# special workflows
-from scripts.extension.segmentation.nucleus_assignments import NucleusAssignmentWorkflow
-from scripts.extension.segmentation.unmerge import UnmergeWorkflow
+from mmpb.extension.segmentation.nucleus_assignments import NucleusAssignmentWorkflow
+from mmpb.extension.segmentation.unmerge import UnmergeWorkflow
# TODO expose this
diff --git a/scripts/segmentation/cilia/__init__.py b/mmpb/segmentation/cilia/__init__.py
similarity index 100%
rename from scripts/segmentation/cilia/__init__.py
rename to mmpb/segmentation/cilia/__init__.py
diff --git a/scripts/segmentation/correction/__init__.py b/mmpb/segmentation/correction/__init__.py
similarity index 100%
rename from scripts/segmentation/correction/__init__.py
rename to mmpb/segmentation/correction/__init__.py
diff --git a/scripts/segmentation/correction/annotation_tool.py b/mmpb/segmentation/correction/annotation_tool.py
similarity index 100%
rename from scripts/segmentation/correction/annotation_tool.py
rename to mmpb/segmentation/correction/annotation_tool.py
diff --git a/scripts/segmentation/correction/assignment_diffs.py b/mmpb/segmentation/correction/assignment_diffs.py
similarity index 100%
rename from scripts/segmentation/correction/assignment_diffs.py
rename to mmpb/segmentation/correction/assignment_diffs.py
diff --git a/scripts/segmentation/correction/cillia_correction_tool.py b/mmpb/segmentation/correction/cillia_correction_tool.py
similarity index 99%
rename from scripts/segmentation/correction/cillia_correction_tool.py
rename to mmpb/segmentation/correction/cillia_correction_tool.py
index 7c0bd7c..63fba36 100644
--- a/scripts/segmentation/correction/cillia_correction_tool.py
+++ b/mmpb/segmentation/correction/cillia_correction_tool.py
@@ -13,7 +13,7 @@ import napari
from heimdall import view, to_source
from elf.io import open_file
-from scripts.files.xml_utils import get_h5_path_from_xml
+from mmpb.files.xml_utils import get_h5_path_from_xml
def xml_to_h5_path(xml_path):
diff --git a/scripts/segmentation/correction/correction_tool.py b/mmpb/segmentation/correction/correction_tool.py
similarity index 100%
rename from scripts/segmentation/correction/correction_tool.py
rename to mmpb/segmentation/correction/correction_tool.py
diff --git a/scripts/segmentation/correction/export_node_labels.py b/mmpb/segmentation/correction/export_node_labels.py
similarity index 100%
rename from scripts/segmentation/correction/export_node_labels.py
rename to mmpb/segmentation/correction/export_node_labels.py
diff --git a/scripts/segmentation/correction/heuristics.py b/mmpb/segmentation/correction/heuristics.py
similarity index 100%
rename from scripts/segmentation/correction/heuristics.py
rename to mmpb/segmentation/correction/heuristics.py
diff --git a/scripts/segmentation/correction/preprocess.py b/mmpb/segmentation/correction/preprocess.py
similarity index 100%
rename from scripts/segmentation/correction/preprocess.py
rename to mmpb/segmentation/correction/preprocess.py
diff --git a/scripts/segmentation/cuticle/__init__.py b/mmpb/segmentation/cuticle/__init__.py
similarity index 100%
rename from scripts/segmentation/cuticle/__init__.py
rename to mmpb/segmentation/cuticle/__init__.py
diff --git a/scripts/segmentation/muscle/__init__.py b/mmpb/segmentation/muscle/__init__.py
similarity index 100%
rename from scripts/segmentation/muscle/__init__.py
rename to mmpb/segmentation/muscle/__init__.py
diff --git a/scripts/segmentation/muscle/muscle_mapping.py b/mmpb/segmentation/muscle/muscle_mapping.py
similarity index 100%
rename from scripts/segmentation/muscle/muscle_mapping.py
rename to mmpb/segmentation/muscle/muscle_mapping.py
diff --git a/scripts/segmentation/muscle/workflow.py b/mmpb/segmentation/muscle/workflow.py
similarity index 100%
rename from scripts/segmentation/muscle/workflow.py
rename to mmpb/segmentation/muscle/workflow.py
diff --git a/scripts/segmentation/nuclei/__init__.py b/mmpb/segmentation/nuclei/__init__.py
similarity index 100%
rename from scripts/segmentation/nuclei/__init__.py
rename to mmpb/segmentation/nuclei/__init__.py
diff --git a/scripts/segmentation/tissue/__init__.py b/mmpb/segmentation/tissue/__init__.py
similarity index 100%
rename from scripts/segmentation/tissue/__init__.py
rename to mmpb/segmentation/tissue/__init__.py
diff --git a/scripts/segmentation/validation/__init__.py b/mmpb/segmentation/validation/__init__.py
similarity index 100%
rename from scripts/segmentation/validation/__init__.py
rename to mmpb/segmentation/validation/__init__.py
diff --git a/scripts/segmentation/validation/eval_cells.py b/mmpb/segmentation/validation/eval_cells.py
similarity index 100%
rename from scripts/segmentation/validation/eval_cells.py
rename to mmpb/segmentation/validation/eval_cells.py
diff --git a/scripts/segmentation/validation/eval_nuclei.py b/mmpb/segmentation/validation/eval_nuclei.py
similarity index 100%
rename from scripts/segmentation/validation/eval_nuclei.py
rename to mmpb/segmentation/validation/eval_nuclei.py
diff --git a/scripts/segmentation/validation/evaluate_annotations.py b/mmpb/segmentation/validation/evaluate_annotations.py
similarity index 100%
rename from scripts/segmentation/validation/evaluate_annotations.py
rename to mmpb/segmentation/validation/evaluate_annotations.py
diff --git a/scripts/segmentation/validation/refine_annotations.py b/mmpb/segmentation/validation/refine_annotations.py
similarity index 100%
rename from scripts/segmentation/validation/refine_annotations.py
rename to mmpb/segmentation/validation/refine_annotations.py
diff --git a/scripts/transformation/__init__.py b/mmpb/transformation/__init__.py
similarity index 100%
rename from scripts/transformation/__init__.py
rename to mmpb/transformation/__init__.py
diff --git a/scripts/transformation/intensity_correction.py b/mmpb/transformation/intensity_correction.py
similarity index 100%
rename from scripts/transformation/intensity_correction.py
rename to mmpb/transformation/intensity_correction.py
diff --git a/scripts/util.py b/mmpb/util.py
similarity index 100%
rename from scripts/util.py
rename to mmpb/util.py
diff --git a/registration/apply_registration.py b/registration/apply_registration.py
index 3d95c75..7b5e404 100644
--- a/registration/apply_registration.py
+++ b/registration/apply_registration.py
@@ -6,7 +6,7 @@ import random
from shutil import rmtree
import luigi
-from scripts.extension.registration import ApplyRegistrationLocal, ApplyRegistrationSlurm
+from mmpb.extension.registration import ApplyRegistrationLocal, ApplyRegistrationSlurm
def apply_registration(input_path, output_path, transformation_file,
diff --git a/segmentation/cell_segmentation.py b/segmentation/cell_segmentation.py
index ec5e6bb..53b5be5 100644
--- a/segmentation/cell_segmentation.py
+++ b/segmentation/cell_segmentation.py
@@ -1,5 +1,5 @@
#! /g/arendt/EM_6dpf_segmentation/platy-browser-data/software/conda/miniconda3/envs/platybrowser/bin/python
-from scripts.segmentation.cells.multicut import workflow
+from mmpb.segmentation.cells.multicut import workflow
# TODO need to expose the path options here
diff --git a/segmentation/compute_default_table.py b/segmentation/compute_default_table.py
index 5fc78ed..e2516fe 100644
--- a/segmentation/compute_default_table.py
+++ b/segmentation/compute_default_table.py
@@ -1,7 +1,7 @@
#! /g/arendt/EM_6dpf_segmentation/platy-browser-data/software/conda/miniconda3/envs/platybrowser/bin/python
import numpy as np
import h5py
-from scripts.attributes.base_attributes import base_attributes
+from mmpb.attributes.base_attributes import base_attributes
def add_max_id():
diff --git a/segmentation/correction/correct_cell_segmentation.py b/segmentation/correction/correct_cell_segmentation.py
index d3b88ac..62c1c7a 100644
--- a/segmentation/correction/correct_cell_segmentation.py
+++ b/segmentation/correction/correct_cell_segmentation.py
@@ -1,12 +1,12 @@
import os
import json
-from scripts.segmentation.correction import (preprocess,
- AnnotationTool,
- CorrectionTool,
- export_node_labels,
- to_paintera_format,
- rank_false_merges,
- get_ignore_ids)
+from mmpb.segmentation.correction import (preprocess,
+ AnnotationTool,
+ CorrectionTool,
+ export_node_labels,
+ to_paintera_format,
+ rank_false_merges,
+ get_ignore_ids)
def run_preprocessing(project_folder):
@@ -104,7 +104,7 @@ def run_correction(project_folder, fm_id_path, scale=2):
def export_correction(project_folder, correct_merges=True, zero_out=True):
- from scripts.segmentation.correction.export_node_labels import zero_out_ids
+ from mmpb.segmentation.correction.export_node_labels import zero_out_ids
p = os.path.join(project_folder, 'data.n5')
in_key = 'node_labels'
diff --git a/segmentation/correction/deprecated.py b/segmentation/correction/deprecated.py
index a03ded7..7b8d060 100644
--- a/segmentation/correction/deprecated.py
+++ b/segmentation/correction/deprecated.py
@@ -24,7 +24,7 @@ def get_skipped_ids(out_path):
def check_export():
- from scripts.segmentation.correction.export_node_labels import check_exported_paintera
+ from mmpb.segmentation.correction.export_node_labels import check_exported_paintera
path1 = '/g/kreshuk/data/arendt/platyneris_v1/data.n5'
assignment_key = 'volumes/paintera/proofread_cells/fragment-segment-assignment'
diff --git a/segmentation/correction/fix_assignments.py b/segmentation/correction/fix_assignments.py
index e8ad6ee..2b7bf8d 100644
--- a/segmentation/correction/fix_assignments.py
+++ b/segmentation/correction/fix_assignments.py
@@ -3,7 +3,7 @@ import json
def get_assignments(version):
- from scripts.segmentation.correction.assignment_diffs import node_labels
+ from mmpb.segmentation.correction.assignment_diffs import node_labels
assert version in ('0.5.5', '0.6.1', 'local')
ws_path = '/g/kreshuk/data/arendt/platyneris_v1/data.n5'
ws_key = 'volumes/paintera/proofread_cells_multiset/data/s0'
@@ -30,7 +30,7 @@ def get_assignments(version):
def get_split_assignments():
import z5py
- from scripts.segmentation.correction.assignment_diffs import assignment_diff_splits
+ from mmpb.segmentation.correction.assignment_diffs import assignment_diff_splits
with z5py.File('./data.n5') as f:
ref = f['assignments/055'][:]
new = f['assignments/corrected'][:]
diff --git a/segmentation/correction/morphology_outlier.py b/segmentation/correction/morphology_outlier.py
index 5a2cdfd..5055e4c 100644
--- a/segmentation/correction/morphology_outlier.py
+++ b/segmentation/correction/morphology_outlier.py
@@ -2,10 +2,10 @@ import os
import json
import numpy as np
import z5py
-from scripts.segmentation.correction import preprocess
-from scripts.segmentation.correction.heuristics import (compute_ratios,
- components_per_slice,
- get_ignore_ids)
+from mmpb.segmentation.correction import preprocess
+from mmpb.segmentation.correction.heuristics import (compute_ratios,
+ components_per_slice,
+ get_ignore_ids)
def run_preprocessing():
diff --git a/segmentation/muscles.py b/segmentation/muscles.py
index 077e1bf..3cd17c1 100644
--- a/segmentation/muscles.py
+++ b/segmentation/muscles.py
@@ -2,8 +2,8 @@
import json
import numpy as np
import pandas as pd
-from scripts.segmentation.muscle import ranked_false_positives, get_mapped_ids
-from scripts.segmentation.muscle.muscle_mapping import compute_labels
+from mmpb.segmentation.muscle import ranked_false_positives, get_mapped_ids
+from mmpb.segmentation.muscle.muscle_mapping import compute_labels
PROJECT_PATH = '/g/kreshuk/pape/Work/muscle_mapping_v1.h5'
diff --git a/segmentation/neuron_traces.py b/segmentation/neuron_traces.py
index cc04ad4..82c8797 100644
--- a/segmentation/neuron_traces.py
+++ b/segmentation/neuron_traces.py
@@ -1,7 +1,7 @@
#! /g/arendt/EM_6dpf_segmentation/platy-browser-data/software/conda/miniconda3/envs/platybrowser/bin/python
import json
import pandas as pd
-from scripts.export import extract_neuron_traces
+from mmpb.export import extract_neuron_traces
# for debugging
diff --git a/segmentation/validation/check_validation.py b/segmentation/validation/check_validation.py
index d85f41f..e09ec08 100644
--- a/segmentation/validation/check_validation.py
+++ b/segmentation/validation/check_validation.py
@@ -1,15 +1,15 @@
import os
import h5py
from heimdall import view, to_source
-from scripts.segmentation.validation import eval_cells, eval_nuclei, get_ignore_seg_ids
+from mmpb.segmentation.validation import eval_cells, eval_nuclei, get_ignore_seg_ids
# ROOT_FOLDER = '../../data'
ROOT_FOLDER = '/g/arendt/EM_6dpf_segmentation/platy-browser-data/data'
def check_cell_evaluation():
- from scripts.segmentation.validation.eval_cells import (eval_slice,
- get_bounding_box)
+ from mmpb.segmentation.validation.eval_cells import (eval_slice,
+ get_bounding_box)
praw = os.path.join(ROOT_FOLDER, 'rawdata/sbem-6dpf-1-whole-raw.h5')
pseg = os.path.join(ROOT_FOLDER, '0.5.5/segmentations/sbem-6dpf-1-whole-segmented-cells-labels.h5')
@@ -57,8 +57,8 @@ def eval_all_cells():
def check_nucleus_evaluation():
- from scripts.segmentation.validation.eval_nuclei import (eval_slice,
- get_bounding_box)
+ from mmpb.segmentation.validation.eval_nuclei import (eval_slice,
+ get_bounding_box)
praw = os.path.join(ROOT_FOLDER, 'rawdata/sbem-6dpf-1-whole-raw.h5')
pseg = os.path.join(ROOT_FOLDER, '0.0.0/segmentations/sbem-6dpf-1-whole-segmented-nuclei-labels.h5')
diff --git a/segmentation/validation/eval_cell_segmentation.py b/segmentation/validation/eval_cell_segmentation.py
index 926f5f8..d2f8bdc 100644
--- a/segmentation/validation/eval_cell_segmentation.py
+++ b/segmentation/validation/eval_cell_segmentation.py
@@ -2,9 +2,9 @@ import argparse
import os
import numpy as np
import h5py
-from scripts.segmentation.validation import eval_cells, get_ignore_seg_ids
-from scripts.attributes.region_attributes import region_attributes
-from scripts.default_config import write_default_global_config
+from mmpb.segmentation.validation import eval_cells, get_ignore_seg_ids
+from mmpb.attributes.region_attributes import region_attributes
+from mmpb.default_config import write_default_global_config
ANNOTATIONS = '../../data/rawdata/evaluation/validation_annotations.h5'
BASELINES = '../../data/rawdata/evaluation/baseline_cell_segmentations.h5'
diff --git a/segmentation/validation/eval_nucleus_segmentation.py b/segmentation/validation/eval_nucleus_segmentation.py
index 98aa0e1..380a71e 100644
--- a/segmentation/validation/eval_nucleus_segmentation.py
+++ b/segmentation/validation/eval_nucleus_segmentation.py
@@ -1,6 +1,6 @@
import argparse
import os
-from scripts.segmentation.validation import eval_nuclei
+from mmpb.segmentation.validation import eval_nuclei
ANNOTATIONS = '../../data/rawdata/evaluation/validation_annotations.h5'
diff --git a/segmentation/validation/proofread_annotations.py b/segmentation/validation/proofread_annotations.py
index a8fb7a0..990db59 100644
--- a/segmentation/validation/proofread_annotations.py
+++ b/segmentation/validation/proofread_annotations.py
@@ -1,6 +1,6 @@
import os
-from scripts.segmentation.validation.refine_annotations import refine, export_refined
-from scripts.segmentation.validation.eval_cells import get_ignore_seg_ids
+from mmpb.segmentation.validation.refine_annotations import refine, export_refined
+from mmpb.segmentation.validation.eval_cells import get_ignore_seg_ids
def proofread(orientation, slice_id):
diff --git a/test/attributes/test_base.py b/test/attributes/test_base.py
index 53a077a..24a7bf8 100644
--- a/test/attributes/test_base.py
+++ b/test/attributes/test_base.py
@@ -18,7 +18,7 @@ class TestBaseAttributes(unittest.TestCase):
pass
def test_base_attributes(self):
- from scripts.attributes.base_attributes import base_attributes
+ from mmpb.attributes.base_attributes import base_attributes
input_path = '../../data/0.0.0/segmentations/sbem-6dpf-1-whole-segmented-nuclei-labels.h5'
input_key = 't00000/s00/0/cells'
diff --git a/test/attributes/test_cell_nucleus_mapping.py b/test/attributes/test_cell_nucleus_mapping.py
index aa1002d..55e735e 100644
--- a/test/attributes/test_cell_nucleus_mapping.py
+++ b/test/attributes/test_cell_nucleus_mapping.py
@@ -22,7 +22,7 @@ class TestCellNucleusMapping(unittest.TestCase):
pass
def test_cell_nucleus_mappings(self):
- from scripts.attributes.cell_nucleus_mapping import map_cells_to_nuclei
+ from mmpb.attributes.cell_nucleus_mapping import map_cells_to_nuclei
segmentation_folder = '../../data/0.1.1/segmentations'
seg_path = os.path.join(segmentation_folder,
diff --git a/test/attributes/test_cilia.py b/test/attributes/test_cilia.py
index 1304a50..c03f3c2 100644
--- a/test/attributes/test_cilia.py
+++ b/test/attributes/test_cilia.py
@@ -6,7 +6,7 @@ import pandas as pd
class TestCilaAttributes(unittest.TestCase):
def test_cilia_attributes(self):
- from scripts.attributes.cilia_attributes import measure_cilia_attributes
+ from mmpb.attributes.cilia_attributes import measure_cilia_attributes
input_path = '../../data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.h5'
input_key = 't00000/s00/0/cells'
diff --git a/test/attributes/test_genes.py b/test/attributes/test_genes.py
index 8ceb547..0c49131 100644
--- a/test/attributes/test_genes.py
+++ b/test/attributes/test_genes.py
@@ -24,9 +24,9 @@ class TestGeneAttributes(unittest.TestCase):
return table
def test_genes(self):
- from scripts.attributes.genes import write_genes_table
- from scripts.extension.attributes import GenesLocal
- from scripts.files import get_h5_path_from_xml
+ from mmpb.attributes.genes import write_genes_table
+ from mmpb.extension.attributes import GenesLocal
+ from mmpb.files import get_h5_path_from_xml
# load original genes table
original_table_file = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/genes.csv'
diff --git a/test/attributes/test_morphology.py b/test/attributes/test_morphology.py
index 1f105c5..caedf7f 100644
--- a/test/attributes/test_morphology.py
+++ b/test/attributes/test_morphology.py
@@ -31,9 +31,9 @@ class TestMorphologyAttributes(unittest.TestCase):
json.dump(conf, f)
def test_nucleus_morphology(self):
- from scripts.attributes.morphology import write_morphology_nuclei
- from scripts.extension.attributes import MorphologyWorkflow
- from scripts.files import get_h5_path_from_xml
+ from mmpb.attributes.morphology import write_morphology_nuclei
+ from mmpb.extension.attributes import MorphologyWorkflow
+ from mmpb.files import get_h5_path_from_xml
self.write_global_config(MorphologyWorkflow.get_config()['global'])
@@ -59,8 +59,8 @@ class TestMorphologyAttributes(unittest.TestCase):
self.assertTrue(np.allclose(table, original_table))
def test_cell_morphology(self):
- from scripts.attributes.morphology import write_morphology_cells
- from scripts.extension.attributes import MorphologyWorkflow
+ from mmpb.attributes.morphology import write_morphology_cells
+ from mmpb.extension.attributes import MorphologyWorkflow
self.write_global_config(MorphologyWorkflow.get_config()['global'])
diff --git a/test/attributes/test_regions.py b/test/attributes/test_regions.py
index 592d6af..7441868 100644
--- a/test/attributes/test_regions.py
+++ b/test/attributes/test_regions.py
@@ -59,7 +59,7 @@ class TestRegions(unittest.TestCase):
self.assertGreater(np.in1d(tis[seg_mask], tis_ids).sum(), 0)
def test_regions(self):
- from scripts.attributes.region_attributes import region_attributes
+ from mmpb.attributes.region_attributes import region_attributes
image_folder = '../../data/0.0.0/images'
segmentation_folder = '../../data/0.0.0/segmentations'
diff --git a/test/cilia.py b/test/cilia.py
index d6db696..574dd8b 100644
--- a/test/cilia.py
+++ b/test/cilia.py
@@ -6,8 +6,7 @@ import h5py
import pandas as pd
from heimdall import view
-from scripts.attributes.cilia_attributes import (compute_centerline,
- get_bb, load_seg)
+from mmpb.attributes.cilia_attributes import compute_centerline, get_bb, load_seg
def view_centerline(raw, obj, path=None):
diff --git a/test/registration/test_wrapper.py b/test/registration/test_wrapper.py
index 3e958a5..663c067 100644
--- a/test/registration/test_wrapper.py
+++ b/test/registration/test_wrapper.py
@@ -6,7 +6,7 @@ import luigi
import numpy as np
import imageio
from shutil import rmtree
-from scripts.extension.registration import ApplyRegistrationLocal
+from mmpb.extension.registration import ApplyRegistrationLocal
class TestRegistrationWrapper(unittest.TestCase):
diff --git a/update_major.py b/update_major.py
index 1995752..4ee5fcb 100755
--- a/update_major.py
+++ b/update_major.py
@@ -5,8 +5,8 @@ import json
import argparse
from subprocess import check_output
-from scripts.files import add_source, copy_release_folder, make_folder_structure, make_bdv_server_file
-from scripts.release_helper import add_data, check_inputs, add_version
+from mmpb.files import add_source, copy_release_folder, make_folder_structure, make_bdv_server_file
+from mmpb.release_helper import add_data, check_inputs, add_version
def get_tags():
diff --git a/update_minor.py b/update_minor.py
index 009b0ad..95e7efc 100755
--- a/update_minor.py
+++ b/update_minor.py
@@ -5,8 +5,8 @@ import json
import argparse
from subprocess import check_output
-from scripts.files import copy_release_folder, make_folder_structure, make_bdv_server_file
-from scripts.release_helper import add_data, check_inputs, add_version
+from mmpb.files import copy_release_folder, make_folder_structure, make_bdv_server_file
+from mmpb.release_helper import add_data, check_inputs, add_version
def get_tags():
diff --git a/update_patch.py b/update_patch.py
index 0761cc7..530e40d 100755
--- a/update_patch.py
+++ b/update_patch.py
@@ -8,12 +8,12 @@ from glob import glob
from shutil import rmtree
from subprocess import check_output, call
-import scripts.attributes
-from scripts.files import get_segmentation_names, get_segmentations
-from scripts.files import (copy_image_data, copy_misc_data, copy_segmentation, copy_tables,
- make_bdv_server_file, make_folder_structure)
-from scripts.export import export_segmentation
-from scripts.release_helper import add_version
+import mmpb.attributes
+from mmpb.files import get_segmentation_names, get_segmentations
+from mmpb.files import (copy_image_data, copy_misc_data, copy_segmentation, copy_tables,
+ make_bdv_server_file, make_folder_structure)
+from mmpb.export import export_segmentation
+from mmpb.release_helper import add_version
def get_tags():
@@ -50,7 +50,7 @@ def update_segmentations(folder, new_folder, names_to_update, target, max_jobs):
def update_table(name, seg_dict, folder, new_folder,
target, max_jobs):
tmp_folder = 'tmp_tables_%s' % name
- update_function = getattr(scripts.attributes, seg_dict['table_update_function'])
+ update_function = getattr(mmpb.attributes, seg_dict['table_update_function'])
update_function(folder, new_folder, name, tmp_folder, seg_dict['resolution'],
target=target, max_jobs=max_jobs)
diff --git a/update_registration.py b/update_registration.py
index a0c0759..6896907 100755
--- a/update_registration.py
+++ b/update_registration.py
@@ -12,14 +12,14 @@ import numpy as np
import pandas as pd
from pybdv import make_bdv
-from scripts.files import copy_release_folder, make_folder_structure, make_bdv_server_file, get_source_names
-from scripts.files.xml_utils import get_h5_path_from_xml, write_simple_xml
-from scripts.release_helper import add_version
-from scripts.extension.registration import ApplyRegistrationLocal, ApplyRegistrationSlurm
-from scripts.default_config import get_default_shebang
-from scripts.attributes.base_attributes import base_attributes
-from scripts.attributes.genes import create_auxiliary_gene_file, gene_assignment_table, vc_assignment_table
-from scripts.util import add_max_id
+from mmpb.files import copy_release_folder, make_folder_structure, make_bdv_server_file, get_source_names
+from mmpb.files.xml_utils import get_h5_path_from_xml, write_simple_xml
+from mmpb.release_helper import add_version
+from mmpb.extension.registration import ApplyRegistrationLocal, ApplyRegistrationSlurm
+from mmpb.default_config import get_default_shebang
+from mmpb.attributes.base_attributes import base_attributes
+from mmpb.attributes.genes import create_auxiliary_gene_file, gene_assignment_table, vc_assignment_table
+from mmpb.util import add_max_id
REGION_NAMES = ('AllGlands',
--
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