Add files to quickstart notebook

examples/quick_start/annotation_tasks_open.yaml

@@ -0,0 +1,23 @@
+# ---------------------------------------
+# Define an annotation task
+# This includes: 
+# 1. a name (e.g., building_simple or rail_space, see below)
+# 2. a list of labels to be used for this task
+# ---------------------------------------
+tasks:
+  phenotype_test:
+    labels: ["No", "Plant"]
+
+# ---------------------------------------
+# paths 
+# You need to specify:
+# 1. a name (e.g., task_test_one_inch_maps_001, see below)
+# 2. patch_paths: path to all the patches to be annotated 
+# 3. parent_paths: path to the original/parent maps/images (which were patchified)
+# 4. annot_dir: directory in which the outputs will be stored
+# ---------------------------------------
+paths:
+  task_test_phenotype:
+    patch_paths: "./dataset/eg_slice_50_50/patch-*PNG"
+    parent_paths: "./dataset/open_access_plant/*png"
+    annot_dir: "./annotations_phenotype_open_access"

examples/quick_start/annotations_phenotype_open_access/phenotype_test_#kasra#.csv

@@ -0,0 +1,100 @@
+image_id,label
+patch-300-350-350-400-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-250-400-300-450-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-300-250-350-300-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-200-400-250-450-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-300-150-350-200-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-300-300-350-350-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-100-300-150-350-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-300-200-350-250-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-100-200-150-250-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-150-350-200-400-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-300-400-350-450-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-0-250-50-300-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-200-350-250-400-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-50-150-100-200-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-250-100-300-150-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-100-250-150-300-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-50-300-100-350-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-400-150-450-200-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-250-450-300-500-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-300-100-350-150-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-200-200-250-250-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-250-150-300-200-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-150-100-200-150-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-200-100-250-150-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-350-250-400-300-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-50-300-100-350-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-350-400-400-450-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-250-300-300-350-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-100-300-150-350-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-300-300-350-350-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-300-100-350-150-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-300-200-350-250-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-450-150-500-200-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-0-300-50-350-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-400-350-450-400-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-100-350-150-400-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-450-200-500-250-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-250-300-300-350-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-150-100-200-150-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-450-150-500-200-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-0-150-50-200-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-250-250-300-300-#2014-06-06_plant001_rgb.png#.PNG,2
+patch-150-200-200-250-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-300-150-350-200-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-450-100-500-150-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-100-450-150-500-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-200-450-250-500-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-400-100-450-150-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-50-350-100-400-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-50-200-100-250-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-150-50-200-100-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-350-450-400-500-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-350-400-400-450-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-200-400-250-450-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-200-100-250-150-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-350-200-400-250-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-50-100-100-150-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-250-350-300-400-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-150-450-200-500-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-100-200-150-250-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-350-50-400-100-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-450-50-500-100-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-400-200-450-250-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-200-50-250-100-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-450-400-500-450-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-200-500-250-530-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-150-350-200-400-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-450-300-500-350-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-250-450-300-500-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-250-50-300-100-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-300-500-350-530-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-0-450-50-500-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-0-500-50-530-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-100-450-150-500-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-100-0-150-50-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-200-0-250-50-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-400-400-450-450-#2014-07-17_plant047_rgb.png#.PNG,2
+patch-0-50-50-100-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-50-500-100-530-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-400-450-450-500-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-200-50-250-100-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-50-50-100-100-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-450-0-500-50-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-350-0-400-50-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-450-450-500-500-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-350-500-400-530-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-100-0-150-50-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-200-0-250-50-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-0-50-50-100-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-50-450-100-500-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-100-50-150-100-#2014-06-06_plant001_rgb.png#.PNG,1
+patch-450-500-500-530-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-350-500-400-530-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-100-500-150-530-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-150-500-200-530-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-400-450-450-500-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-300-500-350-530-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-400-500-450-530-#2014-07-17_plant047_rgb.png#.PNG,1
+patch-0-450-50-500-#2014-07-17_plant047_rgb.png#.PNG,1