From 03d2ac6ab0835f852af9996e5ded12a822ebdc03 Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Thu, 6 Feb 2020 20:52:53 +0100
Subject: [PATCH] Extend bookmark functionality
---
mmpb/bookmarks.py | 53 +++++++++++++++++++++++++++++++++++++----------
1 file changed, 42 insertions(+), 11 deletions(-)
diff --git a/mmpb/bookmarks.py b/mmpb/bookmarks.py
index f4f9bee..d2abb7e 100644
--- a/mmpb/bookmarks.py
+++ b/mmpb/bookmarks.py
@@ -1,21 +1,48 @@
import os
import json
+import pandas as pd
-# TODO change to the proper root folder
-ROOT_FOLDER = '/g/arendt/EM_6dpf_segmentation/platy-browser-data/data/test_n5'
-# TODO allowed values ?
-LAYER_KEYS = {'Color', 'MinValue', 'MaxValue', 'SelectedIds'}
+ROOT_FOLDER = '/g/arendt/EM_6dpf_segmentation/platy-browser-data/data'
+LAYER_KEYS = {'Color', 'MinValue', 'MaxValue',
+ 'SelectedIds', 'Tables'}
+# TODO add all color maps supported by platybrowser
+COLORMAPS = {'Glasbey', 'Viridis'}
+
+
+def validate_tables(table_dict, table_folder):
+ n_color_by = 0
+ for table_name, table_values in table_dict.items():
+ table_file = os.path.join(table_folder, table_name)
+ if not os.path.exists(table_file):
+ return False
+ if table_values:
+ if not len(table_values) == 2:
+ return False
+ table = pd.from_csv(table_file, sep='\t')
+ col, cmap = table_values
+
+ if col not in table.comlumns:
+ return False
+
+ if cmap not in COLORMAPS:
+ return False
+
+ n_color_by += 1
+
+ # can color by maximally 1 column
+ if n_color_by > 1:
+ return False
+
+ return True
def validate_layer(version, name, layer):
- # check that the corresponding file exists
- if 'segmented' in name:
- data_folder = os.path.join(ROOT_FOLDER, version, 'segmentations', 's3-n5')
- else:
- data_folder = os.path.join(ROOT_FOLDER, version, 'images', 's3-n5')
+ # check that the corresponding name exists
+ image_dict = os.path.join(ROOT_FOLDER, version, 'images', 'images.json')
+ with open(image_dict) as f:
+ image_dict = json.load(f)
- file_name = os.path.join(data_folder, name + '.xml')
- if not os.path.exists(file_name):
+ if name not in image_dict:
return False
if not isinstance(layer, dict):
@@ -25,6 +52,10 @@ def validate_layer(version, name, layer):
if len(keys - LAYER_KEYS) > 0:
return False
+ if 'Tables' in keys:
+ table_folder = os.path.join(ROOT_FOLDER, version, image_dict[name]['TableFolder'])
+ return validate_tables(layer['Tables'], table_folder)
+
return True
--
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