Add multi-timepoint qSPECT workflow and improve GE DICOM quantification

[plesqui]

Summary

• Introduces a new workflows/ section for task-oriented processing notebooks, distinct from the guided tutorials.
• Adds a configurable multi-timepoint qSPECT workflow that converts reconstructed SPECT counts to quantitative Bq/mL DICOM images.
• Adds quantitative activity checks and visualization across acquisition time points.
• Improves GE Pixel Scale handling and DICOM UID generation in DicomModify.make_bqml_suv.

Workflow

The new workflows/qSPECT/counts_to_bqml.ipynb notebook:

• Recursively discovers reconstructed SPECT DICOM files while excluding existing qSPECT outputs.
• Supports processing multiple time points from one radiopharmaceutical administration.
• Validates calibration, patient, administration, timing, and scanner-specific inputs before conversion.
• Converts each input independently and records converted, skipped, and failed results.
• Writes _qSPECT.dcm outputs without modifying source files.
• Summarizes acquisition and injection metadata for review.
• Integrates Bq/mL voxel values to calculate total activity within the field of view.
• Compares each FOV measurement against net injected activity physically decayed to its acquisition time, with a 10% tolerance.
• Back-extrapolates the earliest measurement to injection time using physical decay, without fitting.
• Plots measured activity, the first-point back-extrapolation, and the decay-corrected injected-activity tolerance boundary.
• Provides final conversion and quantitative QC checks.

GE quantification

• Reads GE private tag (0011,103B) Pixel Scale and applies it to stored pixels before quantification.
• Defaults Pixel Scale to 1.0 when the tag is absent.
• Supports numeric values stored as either text or raw bytes.
• Rejects invalid, non-finite, zero, or negative Pixel Scale values.
• Reports the applied GE Pixel Scale in the conversion summary.
• Documents the distinction between Pixel Scale and GE projections multiplication, including the need for calibration-matched reconstruction settings.

DICOM robustness

• Generates valid replacement SOP Instance and Series Instance UIDs.
• Preserves the source UID root when it fits DICOM/pydicom limits.
• Falls back to pydicom’s default UID root when the source prefix is too long.
• Keeps MediaStorageSOPInstanceUID synchronized with the generated SOP Instance UID.

Tests and documentation

• Adds tests for missing, valid, byte-encoded, and invalid GE Pixel Scale values.
• Verifies that Pixel Scale is applied to the quantitative mapping.
• Adds coverage for long source UID prefixes and file-meta synchronization.
• Documents workflow usage conventions and the available qSPECT workflow in workflows/README.md.