# Command-line tool
(basics:cli)

Open Zarr filesets containing images with associated OME metadata.
The examples below use the image at http://idr.openmicroscopy.org/webclient/?show=image-6001240.

All examples can be made more or less verbose by passing `-v` or `-q` one or more times:

```bash
ome_zarr -vvv ...
```

## info

Use the `ome_zarr` command to interrogate Zarr datasets.

Remote data:

```bash
ome_zarr info https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr/
```

Local data:

```bash
ome_zarr info 6001240_labels.zarr/
```

## view

Use the `ome_zarr` command to serve local Zarr data and view it in the https://ome.github.io/ome-ngff-validator:

```bash
ome_zarr view 6001240.zarr/

# Use -f or --force to open in browser even if no valid data is found
ome_zarr view 6001240.zarr/ -f
```

## finder

Use the `ome_zarr` command to display multiple OME-Zarr images in the BioFile Finder app
in a browser. This command parses the specified directory to find all OME-Zarr Images
and Plates, combines them into a `biofile_finder.csv` file and opens this in the
app, which allows you to browse thumbnails of all images:

```bash
    ome_zarr finder /path/to/dir/
```

## download

To download all the resolutions and metadata for an image use ``ome_zarr download``. This creates ``6001240.zarr`` locally:

```bash
ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr
```

Specify a different output directory:

```bash
ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr --output image_dir
```

## scale

Use the `ome_zarr scale` command to generate a multiscale pyramid from a Zarr array.
This creates downsampled resolutions of the input image using the specified downsampling method.

Basic usage:

```bash
ome_zarr scale input.zarr output.zarr zyx
```

This reads the input Zarr array with dimensions 'zyx' and writes a multiscale pyramid to the output directory.

Options:

- `--downscale`: The downsampling factor (default: 2). For example, `--downscale 2` creates scale factors of 2, 4, 8, etc.
- `--max_layer`: Maximum number of pyramid levels to generate (default: 4)
- `--method`: Downsampling method to use (default: "resize"). Options are:
    - `nearest`: Nearest neighbor
    - `resize`: Resize with anti-aliasing (default)
    - `laplacian`: Laplacian pyramid
    - `local_mean`: Local mean
    - `zoom`: Scipy zoom
- `--copy-metadata`: If specified, copies the input array metadata to the output group

Example with custom options:

```bash
ome_zarr scale input.zarr output.zarr tczyx --downscale 3 --max_layer 5 --method nearest --copy-metadata
```


## create

To create a sample OME-Zarr image from the `skimage <https://scikit-image.org/docs/stable/api/skimage.data.html>`_
data.

Create an OME-Zarr image in coinsdata.zarr using the 'coins' method in OME-Zarr latest version or v0.4:

```bash
ome_zarr create coinsdata.zarr

ome_zarr create coinsdata.zarr --format 0.4
```

Create an RGB image from the skimage astronaut dataset in testimage.zarr:

```bash
ome_zarr create testimage.zarr --method=astronaut
```

## csv_to_labels

The `csv_to_labels` command uses a CSV file to add key:value properties to labels
under an OME-Zarr Image or Plate.

The OME-Zarr labels metadata must already contain a `properties`
list of `{key:value}` objects, each with a unique key:ID. This key is `omero:shapeId`
in the example below.

This ID can be used to identify a single row of the CSV table by specifying the name of
a column with unique values, e.g. `shape_id` below.
This row is used to add additional column_name:value data to the label properties.

You also need to specify which columns from the CSV to use, e.g. `"area,X,Y,Width,Height"`.
You can also specify the column types (as in https://github.com/ome/omero-metadata/)
to specify the data-type for each column (string by default).

 - `d`: `DoubleColumn`, for floating point numbers
 - `l`: `LongColumn`, for integer numbers
 - `s`: `StringColumn`, for text
 - `b`: `BoolColumn`, for true/false

Use e.g. `#d` as a suffix in the column name to denote a `float` column, no spaces etc.:

```bash
"area#d,label_text#s,Width#l,Height#l"
```

For example, to take values from columns named `area`, `label_text`, `Width` and `Height`
within a CSV file named `labels_data.csv` with an ID column named `shape_id` and add these
values to label properties with an ID key of `omero:shapeId` in an Image or Plate named `123.zarr`:

```bash
ome_zarr csv_to_labels labels_data.csv shape_id "area#d,label_text#s,Width#l,Height#l" 123.zarr omero:shapeId
```