paquo._cli: implement create command

paquo/__main__.py

@@ -2,10 +2,11 @@
 import functools
 import sys
 from contextlib import redirect_stdout
+from itertools import repeat
 from pathlib import Path
 
 from paquo._cli import subcommand, argument, DirectoryType, \
-    config_print_settings, config_print_defaults, list_project, export_annotations
+    config_print_settings, config_print_defaults, list_project, export_annotations, create_project
 from paquo._config import PAQUO_CONFIG_FILENAME, get_searchtree
 
 # noinspection PyTypeChecker
@@ -104,6 +105,51 @@ def list_(args, subparser):
         return 1
 
 
+@subcommand(
+    argument('project_path', nargs='?', default=None, help="path to new qupath project"),
+    argument('--classes', nargs='*', help="path classes to add to project"),
+    argument('--class-colors', nargs='*', help="path class colors in order of classes"),
+    argument('--remove-default-classes', action="store_true", help="don't add default classes"),
+    argument('--images', nargs='*', help="images to add to project"),
+    argument('--force', action="store_true", help="force overwrite existing projects"),
+)
+def create(args, subparser):
+    """create a new qupath project"""
+    if not args.project_path:
+        print(subparser.format_help())
+        return 0
+
+    if args.class_colors and len(args.class_colors) != len(args.classes):
+        print("ERROR: need to specify same number of colors as classes")
+        return 1
+
+    if args.classes and len(args.classes) != len(set(args.classes)):
+        print("ERROR: classes have to be unique")
+        return 1
+
+    class_names_colors = zip(args.classes or [], args.class_colors or repeat(None))
+
+    images = args.images or []
+    for image in images:
+        if not Path(image).is_file():
+            print(f"ERROR: image {image} is not a file")
+            return 1
+
+    try:
+        name = create_project(
+            args.project_path,
+            class_names_colors=class_names_colors,
+            images=images,
+            remove_default_classes=args.remove_default_classes,
+            force_write=args.force
+        )
+    except FileExistsError:
+        print(f"ERROR: project {args.project_path} exists! use --force to overwrite")
+        return 1
+    print(f"project '{name}' created")
+    return 0
+
+
 @subcommand(
     argument('project_path', nargs='?', default=None, help="path to your qupath project file/folder"),
     argument('--image-idx', '-i', required=True, type=int, help="index of a qupath image"),

paquo/_cli.py

@@ -123,6 +123,34 @@ def list_project(path):
                 print(" ".join(line))
 
 
+# -- create related commands -------------------------------------------
+
+def create_project(project_path, class_names_colors, images,
+                   remove_default_classes=False, force_write=False):
+    """create a qupath project"""
+    from paquo.classes import QuPathPathClass
+    from paquo.projects import QuPathProject
+
+    mode = 'x' if not force_write else 'w'
+
+    # noinspection PyTypeChecker
+    with QuPathProject(project_path, mode=mode) as qp:
+        if remove_default_classes:
+            qp.path_classes = ()
+        path_classes = list(qp.path_classes)
+        for name, color in class_names_colors:
+            path_classes.append(
+                QuPathPathClass.create(name, color=color)
+            )
+        qp.path_classes = path_classes
+
+        for image in images:
+            qp.add_image(image)
+
+        name = qp.name
+    return name
+
+
 # -- export related commands -------------------------------------------
 
 def export_annotations(path, image_idx, pretty=False):