Rename python module from scripts to mmpb

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):

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
 

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):

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

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):

analysis/nephridia/morphology.py

 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))

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):

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=''):