# From Eiger HDF5 to CrysAlis outputs

This tutorial explains the end-to-end conversion path used by
`ewoksscxrd`: from Eiger/LImA HDF5 input to CrysAlis-compatible outputs
(`.esperanto`, `.ini`, `.set`, `.ccd`, `.par`, `.run`) plus gallery/EDF products.

## 1. Choose a workflow

Use one of the bundled workflows:

- `src/ewoksscxrd/workflows/demo_eiger2crysalis.json`
- `src/ewoksscxrd/workflows/demo_eiger2crysalis_lima2.json` (dual-threshold with Lima2)

## 2. Inspect task inputs

```bash
ewoks show src/ewoksscxrd/workflows/demo_eiger2crysalis.json
```

This shows you the required workflow inputs (for example
`images`, `output`, `processed_output`, `distance`, `beam`, and optional
`wavelength`/`polarization`).

## 3. Provide the inputs from a script and execute the workflow

The bundled workflow is intentionally generic. You can execute it directly from
Python with explicit runtime `inputs`:

```python
import json
from pathlib import Path

from ewoks import execute_graph

workflow_path = Path("src/ewoksscxrd/workflows/demo_eiger2crysalis_lima2.json")
workflow = json.loads(workflow_path.read_text())

# User-editable values
images = ["/data/.../scan0001/eiger2_frame_0_00000.h5"]
lima2_output = "/data/.../scan0001/eiger2_frame"
esperanto_output = "/data/.../scan0001/frame_{index}.esperanto"
processed_output = "/data/.../scan0001/frame"
par_file = "/data/.../files/scan0001.par"
ini_file = "/data/.../files/CrysalisExpSettings.ini"
set_file = "/data/.../files/scan0001.set"
ccd_file = "/data/.../files/scan0001.ccd"

rotation = None
transpose = False
flip_ud = False
flip_lr = True
energy = None
wavelength = 0.2846
distance = 151.8
beam = [1052, 1102]
polarization = 0.99
kappa = 0
alpha = 50
theta = 0
phi = 0
omega = "-5.000000-index*-0.500000"
dummy = -1
offset = 1
dry_run = False
calc_mask = False
count = 144
omega_start = -35
omega_end = 35
domega = 1

# Currently the run file task expects a dict with all the processing parameters.
run_parameters = {
    "count": count,
    "omega_start": omega_start,
    "omega_end": omega_end,
    "domega": domega,
    "flip_ud": flip_ud,
    "flip_lr": flip_lr,
    "wavelength": wavelength,
    "distance": distance,
    "beam": beam,
    "polarization": polarization,
    "kappa": kappa,
    "alpha": alpha,
    "theta": theta,
    "phi": phi,
    "omega": omega,
    "rotation": rotation,
    "dummy": dummy,
    "offset": offset,
    "dry_run": dry_run,
    "calc_mask": calc_mask,
}

inputs = [
    {
        "name": "images",
        "value": images,
        "task_identifier": "ewoksscxrd.tasks.lima2thresholding.Lima2Thresholding",
    },
    {
        "name": "output",
        "value": lima2_output,
        "task_identifier": "ewoksscxrd.tasks.lima2thresholding.Lima2Thresholding",
    },
    {
        "name": "scale_factor",
        "value": 1,
        "task_identifier": "ewoksscxrd.tasks.lima2thresholding.Lima2Thresholding",
    },
    {
        "name": "output",
        "value": esperanto_output,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "processed_output",
        "value": processed_output,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "rotation",
        "value": rotation,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "transpose",
        "value": transpose,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "flip_ud",
        "value": flip_ud,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "flip_lr",
        "value": flip_lr,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "energy",
        "value": energy,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "wavelength",
        "value": wavelength,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "distance",
        "value": distance,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "beam",
        "value": beam,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "polarization",
        "value": polarization,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "kappa",
        "value": kappa,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "alpha",
        "value": alpha,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "theta",
        "value": theta,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "phi",
        "value": phi,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "omega",
        "value": omega,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "dummy",
        "value": dummy,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "offset",
        "value": offset,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "dry_run",
        "value": dry_run,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "calc_mask",
        "value": calc_mask,
        "task_identifier": "ewoksscxrd.tasks.eiger2crysalis.Eiger2Crysalis",
    },
    {
        "name": "par_file",
        "value": par_file,
        "task_identifier": "ewoksscxrd.tasks.createparfiles.CreateParFiles",
    },
    {
        "name": "ini_file",
        "value": ini_file,
        "task_identifier": "ewoksscxrd.tasks.createinifiles.CreateIniFiles",
    },
    {
        "name": "ccd_set_file",
        "value": set_file,
        "task_identifier": "ewoksscxrd.tasks.createsetccdfiles.CreateSetCcdFiles",
        "id": "3",
    },
    {
        "name": "ccd_set_file",
        "value": ccd_file,
        "task_identifier": "ewoksscxrd.tasks.createsetccdfiles.CreateSetCcdFiles",
        "id": "4",
    },
    {
        "name": "run_parameters",
        "value": run_parameters,
        "task_identifier": "ewoksscxrd.tasks.createrunfiles.CreateRunFiles",
    },
]

execute_graph(
    workflow,
    inputs=inputs,
    convert_destination="executed_demo_eiger2crysalis.json",
    merge_outputs=False,
)
```

## 4. Execute the workflow

```bash
python run_eiger2crysalis.py
```

Once the workflow is executed, it is converted with all the provided inputs into a json file. The name and path of the json file is defined in `convert_destination` (i.e. `executed_demo_eiger2crysalis.json` in this case).

## 5. Validate produced files

A typical processed output tree looks like:

```text
PROCESSED_DATA/sample/sample_dataset/scan0001/
  CrysalisExpSettings.ini
  gallery/sample_dataset_0001_average.png
  sample_dataset_0001_1_1.esperanto
  ...
  sample_dataset_0001.ccd
  sample_dataset_0001.par
  sample_dataset_0001.run
  sample_dataset_0001.set

PROCESSED_DATA/sample/edf_PX/
  sample_dataset_0001.edf
```

The exact names depend on your scan and workflow inputs.

## 6. Data Portal visibility

If the `DataPortal` task runs with valid context/credentials, processed data can
be published and browsed in the Data Portal with gallery preview and files.

```{note}
Data Portal publication depends on runtime environment and ICAT connectivity.
This onlys works when executeing the workflow on ESRF premises.
```