From 85d2a86d970ee86bba1f8e1054557737716add6d Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 7 Nov 2019 17:41:38 +0100
Subject: [PATCH] Add functionality to autogenerate additional table file and
add it to 0.6.3
---
.../additional_tables.txt | 1 +
.../additional_tables.txt | 6 ++++
.../additional_tables.txt | 2 ++
.../additional_tables.txt | 2 ++
scripts/attributes/base_attributes.py | 28 +++++++++++++++++++
scripts/attributes/master.py | 8 +++++-
scripts/files/copy_helper.py | 3 ++
7 files changed, 49 insertions(+), 1 deletion(-)
create mode 100644 data/0.6.3/tables/prospr-6dpf-1-whole-virtual-cells-labels/additional_tables.txt
create mode 100644 data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cells-labels/additional_tables.txt
create mode 100644 data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cilia-labels/additional_tables.txt
create mode 100644 data/0.6.3/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/additional_tables.txt
diff --git a/data/0.6.3/tables/prospr-6dpf-1-whole-virtual-cells-labels/additional_tables.txt b/data/0.6.3/tables/prospr-6dpf-1-whole-virtual-cells-labels/additional_tables.txt
new file mode 100644
index 0000000..fa898e9
--- /dev/null
+++ b/data/0.6.3/tables/prospr-6dpf-1-whole-virtual-cells-labels/additional_tables.txt
@@ -0,0 +1 @@
+profile_clust_curated.csv
diff --git a/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cells-labels/additional_tables.txt b/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cells-labels/additional_tables.txt
new file mode 100644
index 0000000..5f8b18c
--- /dev/null
+++ b/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cells-labels/additional_tables.txt
@@ -0,0 +1,6 @@
+cells_to_nuclei.csv
+extrapolated_intensity_correction.csv
+genes.csv
+morphology.csv
+regions.csv
+vc_assignments.csv
diff --git a/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cilia-labels/additional_tables.txt b/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cilia-labels/additional_tables.txt
new file mode 100644
index 0000000..7f85507
--- /dev/null
+++ b/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-cilia-labels/additional_tables.txt
@@ -0,0 +1,2 @@
+cell_mapping.csv
+morphology.csv
diff --git a/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/additional_tables.txt b/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/additional_tables.txt
new file mode 100644
index 0000000..acc707e
--- /dev/null
+++ b/data/0.6.3/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/additional_tables.txt
@@ -0,0 +1,2 @@
+extrapolated_intensity_correction.csv
+morphology.csv
diff --git a/scripts/attributes/base_attributes.py b/scripts/attributes/base_attributes.py
index fad0384..1df9f1a 100644
--- a/scripts/attributes/base_attributes.py
+++ b/scripts/attributes/base_attributes.py
@@ -160,6 +160,34 @@ def base_attributes(input_path, input_key, output_path, resolution,
return label_ids
+def write_additional_table_file(table_folder):
+ # get all the file names in the table folder
+ file_names = os.listdir(table_folder)
+ file_names.sort()
+
+ # make sure we have the default table
+ default_name = 'default.csv'
+ if default_name not in file_names:
+ raise RuntimeError("Did not find the default table ('default.csv') in the table folder %s" % table_folder)
+
+ # don't write anything if we don't have additional tables
+ if len(file_names) == 1:
+ return
+
+ # write file for the additional tables
+ out_file = os.path.join(table_folder, 'additional_tables.txt')
+ with open(out_file, 'w') as f:
+ for name in file_names:
+ ext = os.path.splitext(name)[1]
+ # only add csv files
+ if ext != '.csv':
+ continue
+ # don't add the default table
+ if name == 'default.csv':
+ continue
+ f.write(name + '\n')
+
+
# TODO this is un-tested !!!
def propagate_attributes(id_mapping_path, old_table_path, output_path):
""" Propagate all attributes to new ids. (column label id)
diff --git a/scripts/attributes/master.py b/scripts/attributes/master.py
index df607d9..7541b4c 100644
--- a/scripts/attributes/master.py
+++ b/scripts/attributes/master.py
@@ -1,7 +1,7 @@
import os
import h5py
-from .base_attributes import base_attributes, propagate_attributes
+from .base_attributes import base_attributes, propagate_attributes, write_additional_table_file
from .cell_nucleus_mapping import map_cells_to_nuclei
from .genes import gene_assignment_table, vc_assignment_table
from .morphology import write_morphology_cells, write_morphology_nuclei
@@ -84,6 +84,8 @@ def make_cell_tables(old_folder, folder, name, tmp_folder, resolution,
extrapol_mask, 't00000/s00/0/cells',
extrapol_out, tmp_folder, target, max_jobs)
+ write_additional_table_file(table_folder)
+
def make_nucleus_tables(old_folder, folder, name, tmp_folder, resolution,
target='slurm', max_jobs=100):
@@ -117,6 +119,8 @@ def make_nucleus_tables(old_folder, folder, name, tmp_folder, resolution,
extrapol_mask, 't00000/s00/0/cells',
extrapol_out, tmp_folder, target, max_jobs)
+ write_additional_table_file(table_folder)
+
def make_cilia_tables(old_folder, folder, name, tmp_folder, resolution,
target='slurm', max_jobs=100):
@@ -144,3 +148,5 @@ def make_cilia_tables(old_folder, folder, name, tmp_folder, resolution,
cilia_morphology(seg_path, seg_key,
base_out, morpho_out, resolution,
tmp_folder, target=target, max_jobs=max_jobs)
+
+ write_additional_table_file(table_folder)
diff --git a/scripts/files/copy_helper.py b/scripts/files/copy_helper.py
index 9d6c570..b7c6ad3 100644
--- a/scripts/files/copy_helper.py
+++ b/scripts/files/copy_helper.py
@@ -2,6 +2,7 @@ import os
import shutil
from .xml_utils import copy_xml_with_newpath, get_h5_path_from_xml
from .sources import get_image_names, get_segmentation_names, get_segmentations
+from ..attributes.base_attributes import write_additional_table_file
def copy_file(xml_in, xml_out):
@@ -28,6 +29,8 @@ def copy_tables(src_folder, dst_folder, name):
rel_path = os.path.relpath(src_file, table_out)
if not os.path.exists(dst_file):
os.symlink(rel_path, dst_file)
+ # write the txt file for additional tables
+ write_additional_table_file(dst_folder)
def copy_segmentation(src_folder, dst_folder, name):
--
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