Preflight check

Purpose. Verify that all essential acquisition metadata were parsed from the raw files and let the user complete or correct missing values before running peak finding / centering / indexing. All fields are persisted back into the dataset .ini under [AcquisitionDetails].

How it works

• Reads from: <dataset>.ini → [AcquisitionDetails]

• Writes to: the same section, immediately on edit (per-field textChanged handlers)

• Also inspects <dataset>.h5 to detect if a pixel mask exists (/mask)

Fields shown

Label (UI)	INI key	Unit shown (UI)	Notes
Acceleration Voltage	acceleration_voltage	kV	UI displays kV, but stores volts in INI (auto-converted).
Camera Length	camera_length	m	Read-only; you can apply a correction factor (see below).
Camera Length Correction Factor	camera_length_correction	–	Editable multiplier, default 1. Saved to INI immediately.
Resolution (width × height)	resolution_width/height	px	Read-only.
Bin Factor (width × height)	binning_width/height	–	Read-only.
Binned Resolution (computed)	(no INI key; display only)	px	Auto-updates from resolution ÷ bin factor.
Exposure Time	exposure_time	s	Read-only.
ADU	adu_per_photon	–	Detector gain factor used in CrystFEL geometry (adu_per_photon).
Pixels per Meter	pixels_per_meter	m⁻¹	If empty, Calculate button is enabled (see below).

Editable vs. read-only.

• Fields with existing values are read-only to prevent accidental edits.

• Empty fields become editable so the user can complete missing metadata.

• camera_length_correction is always editable.

• Click Edit Metadata to unlock all fields for manual correction (useful when the imported value is wrong). A confirmation dialog warns if downstream processing results already exist.

Pixels-per-meter calculator

Click Calculate to open the PixelCalc dialog:

• Detector presets:
  Dectris ELA, Dectris SINGLA, Gatan OneView, Thermo Fisher Ceta-D, Thermo Fisher Ceta-S, Timepix3/Medipix3, Other.
  Presets fill the physical pixel size (µm) and lock the field; Other lets you type a custom value.

• Bin Factor: prefilled from binning_width (you can edit).

• Formula:
  [ \text{pixels_per_meter} ;=; \frac{1}{\text{pixel_size (m)} \times \text{bin_factor}} ]

• The dialog live-updates the main window’s pixels_per_meter field and saves it to the INI.

If pixels_per_meter already exists, the Calculate button is disabled (to avoid accidental override). Clear the field to re-enable.

Pixel mask controls

• Mask from Image… → choose a bitmap (.bmp/.png/.jpg), COSEDA creates a mask via pixmask.generate_mask(...) and saves it to <dataset>.h5:/mask.

• Remove Mask → deletes /mask from the HDF5.

• Generate Full Mask → writes a full-valid mask to /mask.

Auto-UI: If /mask exists, Remove Mask is shown and Full Mask is hidden; otherwise the reverse.

Note: A pixel mask is required before running Peak Finding. If no mask is present, the Peakfinding window will block the run and prompt you to generate one first. Use Generate Full Mask if you have no beamstop or bad pixels to exclude.

Additional controls

• Apply to Workspace → copy the current [AcquisitionDetails] metadata (and mask, if present) to all INI files loaded in the workspace. Useful when multiple datasets share the same acquisition conditions.

• Edit Metadata → unlock read-only fields for manual correction. A warning is shown if downstream processing results already exist for the dataset.

Geometry interaction: Mask validity is still defined in raw detector pixels. If detector geometry remapping is enabled later, masking is applied to raw-frame intensities first; panel geometry then controls where remaining pixels are placed in corrected display/analysis coordinates.

Completion check

The Preflight Check is considered “complete” when all of these have values:

• acceleration_voltage (kV shown; stored in V)

• camera_length (m)

• camera_length_correction

• resolution_width, resolution_height (px)

• binning_width, binning_height

• pixels_per_meter (m⁻¹)

Use Calculate to fill pixels_per_meter if missing. After completion, close the dialog and proceed with Peak Finding.

Using the GUI

Open Preflight Check from the toolbar or menu.

1. Review the metadata fields. Empty fields are editable; fill in any missing values.

2. If pixels_per_meter is empty, click Calculate, select your detector preset (or enter a custom pixel size), and confirm. The field is updated live and saved to the INI.

3. If no pixel mask exists, click Generate Full Mask (or Mask from Image… to load a beamstop mask from a bitmap).

4. Optionally click Apply to Workspace to copy the current [AcquisitionDetails] metadata and mask to all datasets loaded in the workspace.

5. Close the dialog and proceed with Peak Finding.

If you need to correct a value that was imported incorrectly, click Edit Metadata to unlock all read-only fields. A warning dialog appears if downstream results already exist.

Tips

• Units: The UI label for Camera Length is meters; ensure your upstream importers wrote meters (not mm). If your microscope reports mm (1700 m camera length might be a bit much ;-), convert or store a correction via camera_length_correction.

• Voltage unit conversion: The UI shows kV, but the INI is stored in volts (the dialog converts kV→V on save).

• Binned resolution: This is display-only; it’s computed as resolution ÷ bin. If the import didn’t set binning, fix that first.

• INI writes are immediate: Every edit persists to disk; no extra “Save” button.

• Mask presence: The Remove/Full buttons toggle after file changes; if you manipulate the HDF5 externally, reopen the dialog to refresh.