Issue #47 and other

[matthewrdiamond]

• Added input validation, including helper functions
• Added load_file_indices callback
• Updated check_filenames to populate the field

[matthewrdiamond]

# Wire Reconstruction Validation Checks

This document lists all validation checks performed by `validate_wire_reconstruction_inputs` in `create_wire_reconstruction.py`.

## Global Parameter Validation

### 1. Root Path
- Root path is required (empty or None)
- Root path directory exists (directory does not exist at path)

### 2. Data Path
- Data path is required (empty or None)
- Data path parsing succeeds (parse_parameter raises ValueError)

### 3. All Other Parameters
For each parameter: `filenamePrefix`, `scanPoints`, `geoFile`, `depth_start`, `depth_end`, `depth_resolution`, `percent_brightest`, `outputFolder`, `scanNumber`, `wire_edges`, `author`

- Parameter is not missing/empty (value is None, empty string, or falsy except 0 for numeric fields)
- Parameter parsing succeeds (parse_parameter raises ValueError)
- Parameter count matches number of inputs (parsed list length ≠ number of data paths)

**Note**: `scanNumber` generates warnings instead of errors for all checks

## Per-Input Validation

### 4. Depth Parameters
- Depth start is required (empty for this input)
- Depth start is valid number (cannot convert to float)
- Depth end is required (empty for this input)
- Depth end is valid number (cannot convert to float)
- Depth resolution is required (empty for this input)
- Depth resolution is valid number (cannot convert to float)
- Depth start < depth end (depth_start ≥ depth_end)
- Large depth range warning (depth_end - depth_start > 500 µm)
- Depth resolution is positive (depth_resolution ≤ 0)
- Very small depth resolution warning (depth_resolution < 0.1 µm)
- Depth resolution < depth range (depth_resolution > |depth_end - depth_start|)

### 5. Intensity Percentile
- Intensity percentile is required (empty for this input)
- Intensity percentile is valid number (cannot convert to float)
- Intensity percentile in valid range (value ≤ 0 or > 100)

### 6. Geometry File
- Geometry file is required (empty for this input)
- Geometry file exists (file does not exist at root_path/geoFile)

### 7. Output Folder
- Output folder is required (empty for this input)
- Output folder already exists warning (directory exists at root_path/outputFolder, skipped if contains %d)

### 8. Data Files
- Data directory exists (directory does not exist at root_path/data_path)
- Data directory contains files (directory exists but contains no files)
- Catalog path matches warning (catalog database has different path for this scan number)
- Files match prefix pattern (no files match filenamePrefix pattern with wildcard substitution)
- Files match specific scan points (files missing for specific scan point numbers in scanPoints)
- Invalid scan points format (srange parsing fails for scanPoints)

### 9. Scan Number
- Scan number is valid integer warning (cannot verify .isdigit())

## Summary

**Total Checks**: ~30 global + ~25 per input

**Result Structure**:
```python
{
    'heading': str,  # "Validation Error!" | "Validation Warning!" | "Validation Success!"
    'errors': list,
    'warnings': list,
    'field_highlights': dict  # {field_id: 'error'|'warning'}
}

Special Cases:

• scanNumber: All failures are warnings (non-blocking)
• outputFolder: Existence check skipped if contains %d placeholder
• Early return on data_path parsing failure
• Multiple inputs: Checks run per input with "Input {i+1}:" prefix

[matthewrdiamond]

scanNumber has hard-coded exemptions (warnings instead of errors)

[matthewrdiamond]

Also, a missing '*' was added to the glob call to find for matching files in submit_parameters().