added script

pyproject.toml

@@ -26,6 +26,7 @@ classifiers = [
 requires = [
     "sensospot_data",
     "Pillow >= 8.0",
+    "click",
 ]
 requires-python = ">=3.7"
 
@@ -47,6 +48,9 @@ dev = [
     "pre-commit",
 ]
 
+[tool.flit.scripts]
+sensospot_images = "sensospot_images:run"
+
 [tool.black]
 line-length = 79
 py37 = true

sensospot_images/__init__.py

@@ -5,18 +5,24 @@ Creating nice spot images from scans
 
 __version__ = "0.0.1"
 
-from pathlib import Path
 import sys
+from pathlib import Path
+from datetime import datetime
 
+import click
 from sensospot_data import parse_file
 from sensospot_data.parameters import _search_measurement_params_file
 
-from .images import recalculate, get_position, annotate_image, load_array_image, crop
+from .images import (
+    crop,
+    recalculate,
+    get_position,
+    annotate_image,
+    load_array_image,
+)
 from .parameters import get_spot_parameters, get_array_parameters
 
 
-
-
 def calulate_pixel_size(data_frame, array_definition):
     first = get_position(data_frame.iloc[0], actual=False)
     last = get_position(data_frame.iloc[-1], actual=False)
@@ -47,7 +53,7 @@ def get_example_data_path(input_dir):
     tif_files = input_path.glob("*.tif")
     example_tif = next(tif_files)
     return example_tif.with_suffix(".csv")
-    
+
 
 def get_filename_prefix(input_dir):
     file_path = get_example_data_path(input_dir)
@@ -60,17 +66,18 @@ def retrieve_spot_parameters(input_dir, scale):
     parameters_path = _search_measurement_params_file(input_dir)
     if parameters_path is None:
         sys.exit(f"Could not find parameter files in {input_dir}")
-    
+
     array_parameters = get_array_parameters(parameters_path)
     spot_parameters = get_spot_parameters(parameters_path, array_parameters)
-    
+
     example_data_path = get_example_data_path(input_dir)
     example_data = parse_file(example_data_path)
 
     pixel_size = calulate_pixel_size(example_data, array_parameters)
-    
+
     return recalculate(spot_parameters, scale / pixel_size)
 
+
 def search_image_files(input_dir, wells, exposures):
     input_path = Path(input_dir)
     prefix = get_filename_prefix(input_path)
@@ -78,6 +85,7 @@ def search_image_files(input_dir, wells, exposures):
     pattern = tmp_pattern.replace("***", "*").replace("**", "*")
     return input_path.glob(pattern)
 
+
 def create_file_map(input_dir, wells, exposures):
     file_map = {}
     for tif_path in search_image_files(input_dir, wells, exposures):
@@ -89,19 +97,31 @@ def create_file_map(input_dir, wells, exposures):
             file_map[csv_path].append(tif_path)
     return file_map
 
+
 def process_image(image_file, spot_parameters, spot_data, scale):
     img = load_array_image(image_file, scale=scale)
     annotate_image(img, spot_parameters, spot_data, scale)
     return img
 
-def create_crops(output_path, img, image_path, spot_parameters, array_data, scale):
+
+def create_crops(
+    output_path, img, image_path, spot_parameters, array_data, scale
+):
     base_name = image_path.stem
     for index, spot_data in array_data.iterrows():
         cropped_img = crop(img, spot_parameters, spot_data, scale)
         new_path = output_path / f"{base_name}_{index + 1:03}.tif"
         cropped_img.save(new_path)
 
-def process(input_dir, output_dir, scale=3, wells="*", exposures="*", add_single_spots=False):
+
+def process(
+    input_dir,
+    output_dir,
+    wells="*",
+    exposures="*",
+    scale=3,
+    add_single_spots=False,
+):
     spot_parameters = retrieve_spot_parameters(input_dir, scale)
     file_map = create_file_map(input_dir, wells, exposures)
     output_path = Path(output_dir)
@@ -114,5 +134,65 @@ def process(input_dir, output_dir, scale=3, wells="*", exposures="*", add_single
             img = process_image(image_path, spot_parameters, array_data, scale)
             img.save(output_path / image_path.name)
             if add_single_spots:
-                create_crops(output_path, img, image_path, spot_parameters, array_data, scale)
+                create_crops(
-
+                    output_path,
+                    img,
+                    image_path,
+                    spot_parameters,
+                    array_data,
+                    scale,
+                )
+
+
+@click.command()
+@click.argument(
+    "source",
+    type=click.Path(
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+        writable=True,
+    ),
+)
+@click.option(
+    "-o",
+    "--output",
+    default=None,
+    help="Output directory name, defaults to folder on desktop",
+)
+@click.option(
+    "-w",
+    "--wells",
+    default="*",
+    help="restrict to this wells, * = all",
+)
+@click.option(
+    "-e",
+    "--Exposures",
+    default="*",
+    help="restrict to this exposure ids, * = all",
+)
+@click.option(
+    "-s",
+    "--scale",
+    type=int,
+    default=3,
+    help="scale-up of images",
+)
+@click.option(
+    "--spots",
+    default=False,
+    is_flag=True,
+    help="include cropped images of spots",
+)
+def run(source, output=None, wells="*", exposures="*", scale=3, spots=False):
+    if output is None or not Path(output).is_dir():
+        default = Path.home() / "Desktop"
+        if not default.is_dir():
+            default = Path.home()
+        now = datetime.now().strftime("%Y-%m-%d %H-%M-%S")
+        output = default / now
+        output.mkdir(exist_ok=True)
+
+    process(source, output, wells, exposures, scale, spots)