revamped readme

README.md

@@ -1,15 +1,37 @@
 Sensospot Images
 ================
 
-Creating nice spot images from scans
+Creating nice grid images from scans
 
 ## Example:
 
-```python
+```sh
 
-    import sensospot_grid
+    > sensospot_grid /path/to/sensospot/raw/data/folder
+```
+
+## Help:
+
+```sh
+    > sensospot_grid --help
+    Usage: sensospot_grid [OPTIONS] SOURCE
+
+    command line interface to process a complete raw data directory
+
+    source: the raw data directory output: directory to store the cropped
+    images in wells: glob pattern for well matching exposures: glob pattern
+    for exposure id matching scale: scale factor for the output images crop:
+    create cropped images for each spot
+
+    Options:
+    -o, --output TEXT     Output directory name, defaults to new folder in
+                            parent of source
 
-    sensospot_grid.run()
+    -w, --wells TEXT      restrict to this wells, * = all  [default: *]
+    -e, --Exposures TEXT  restrict to this exposure ids, * = all  [default: *]
+    -s, --scale INTEGER   scale-up of images  [default: 3]
+    --crop                create cropped images of each spots  [default: False]
+    --help                Show this message and exit.
 ```