Add PhaseEncodingDirection and EchoNumber to files and mri_violations_log insert statements

[cmadjar]

Description

This PR updates all imaging pipelines to add the PhaseEncodingDirection and EchoNumber information when present in the insertion of new rows into the files and mri_violations_log tables.

Resolves #784

Caveat for existing project

Make sure to source the SQL patches attached to aces/Loris#8152 or source the SQL release patch from 24.0.0 to 24.1.0 releases of LORIS.

[cmadjar]

Tests run:

Python dcm2bids pipeline

• insert file with same EchoTime/SeriesUID but different PhaseEncodingDirection (HBCD GE pilot data) in the files table

MariaDB [loris]> select SeriesUID, EchoTime, PhaseEncodingDirection, EchoNumber from files where PhaseEncodingDirection is not null;;
+-----------------------------------------------------------+----------+------------+------------------------+
| SeriesUID                                                 | EchoTime | EchoNumber | PhaseEncodingDirection |
+-----------------------------------------------------------+----------+------------+------------------------+
| 1.2.840.113619.2.408.5282380.5215077.27238.1655150882.584 |     0.08 | NULL       | j-                     |
| 1.2.840.113619.2.408.5282380.5215077.27238.1655150882.584 |     0.08 | NULL       | j                      |
+-----------------------------------------------------------+----------+------------+------------------------+

• insert file with same EchoTime/SeriesUID but different EchoNumber (HBCD GE pilot data) in the files table

MariaDB [loris]> select SeriesUID, EchoTime, PhaseEncodingDirection, EchoNumber from files where EchoNumber is not null;
+-----------------------------------------------------------+----------+------------+------------------------+
| SeriesUID                                                 | EchoTime | EchoNumber | PhaseEncodingDirection |
+-----------------------------------------------------------+----------+------------+------------------------+
| 1.2.840.113619.2.408.5282380.5215077.27238.1655150882.602 | 0.000472 | 1          | NULL                   |
+-----------------------------------------------------------+----------+------------+------------------------+

• insert file with same EchoTime/SeriesUID but different PhaseEncodingDirection (HBCD GE pilot data) in the mri_violations_log table

MariaDB [loris]> select SeriesUID, EchoTime, PhaseEncodingDirection, EchoNumber from mri_violations_log where PhaseEncodingDirection is not null; 
+-----------------------------------------------------------+----------+------------+------------------------+
| SeriesUID                                                 | EchoTime | EchoNumber | PhaseEncodingDirection |
+-----------------------------------------------------------+----------+------------+------------------------+
| 1.2.840.113619.2.408.5282380.5215077.27238.1655150882.584 |     0.08 | NULL       | j                      |
+-----------------------------------------------------------+----------+------------+------------------------+

• insert file with same EchoTime/SeriesUID but different EchoNumber (HBCD GE pilot data) in the mri_violations_log table

MariaDB [loris]> select SeriesUID, EchoTime, PhaseEncodingDirection, EchoNumber from mri_violations_log where EchoNumber is not null; 
+-----------------------------------------------------------+----------+------------------------+------------+
| SeriesUID                                                 | EchoTime | PhaseEncodingDirection | EchoNumber |
+-----------------------------------------------------------+----------+------------------------+------------+
| 1.2.840.113619.2.408.5282380.5215077.27238.1655150882.602 | 0.000472 | NULL                   | 2          |
+-----------------------------------------------------------+----------+------------------------+------------+

Python BIDS import pipeline

• on a BIDS dataset with EchoTime/SeriesUID/EchoNumber/PhaseEncodingDirection set in one modality and ensure proper fields are set in the files table

Perl dcm2mnc pipeline

• insert file with same EchoTime/SeriesUID but different PhaseEncodingDirection (HBCD GE pilot data) in the files table
• insert file with same EchoTime/SeriesUID but different EchoNumber (HBCD GE pilot data) in the files table
• insert file with same EchoTime/SeriesUID but different PhaseEncodingDirection (HBCD GE pilot data) in the mri_violations_log table
• insert file with same EchoTime/SeriesUID but different EchoNumber (HBCD GE pilot data) in the mri_violations_log table