leonarski_f
54f2de31bb
A grid scan is a set of stills at a stationary spindle, and the angle it stood at is what relates one grid to another taken elsewhere on the circle. Users were finding an all-zero omega in the file and concluding the angle could not be recorded at all. It already can, and has since the goniometer and the grid scan stopped being alternatives: send the axis with step 0 and its start angle, and that angle is written per image into the NXmx sample chain, read back by reader/, and taken by dials.import as a set of stills. Measured on a generated 12-image grid: the placeholder file carries omega = 0 x 12, the same file with the axis sent at step 0 carries omega = 90 x 12, and dials.import reports "still: 1, sweep: 0" for both. Nothing in the code needed changing, so nothing was; what was missing was that nobody could tell, and that no test held the behaviour down. So: the API and the HDF5 documentation now say it in as many words, and three tests pin the three legs the value crosses - the OpenAPI request (which used to drop the grid scan whenever an axis was present, unpinned until now), the CBOR start message, and the file round trip. Also corrects a claim two comments and the HDF5 page were making. NXmx can express "no rotation" perfectly well - a sample may depend_on "." - so the placeholder is not there for the standard's sake. It is there because dxtbx cannot read a sample chain of translations alone: strip the rotation axis from a grid scan master and dials.import dies in get_dxtbx_goniometer with a matmul dimension mismatch. Recorded so nobody removes the placeholder on the strength of the standard. One thing the change does not fix, because it cannot: a stationary angle is invisible to DIALS when a grid scan is present. dxtbx picks the first varying axis as the scan axis, which is a grid translation, so the oscillation reads (0, 0); and with exactly one rotation axis in the chain it builds a single-axis goniometer whose fixed rotation is the identity, never consulting the angle. The same angle IS visible when it is the only candidate (oscillation reads (90, 0)) or when a Smargon head puts a second rotation axis in the chain (the setting rotation then carries it). The value is in the file and correct either way.
1.8 KiB
1.8 KiB
GridScan
Definition of a grid scan. Combine it with a goniometer axis to state the angle the spindle stood at: send goniometer with step 0 and the start angle of the grid scan, and that angle is written per image into the NXmx sample transformation chain. Without one the spindle is recorded at 0, which says that nobody stated an angle rather than that the spindle stood at 0.
Properties
| Name | Type | Description | Notes |
|---|---|---|---|
| n_fast | int | Number of elements in the fast direction | |
| step_x_um | float | Step in grid along the fast direction. Can be negative. Positive number: left to right Negative number: right to left | |
| step_y_um | float | Step in grid along the slow direction. Can be negative. Positive number: top to bottom Negative number: bottom to top | |
| vertical | bool | If disabled: fast direction = X, slow direction = Y If enabled: fast direction = Y, slow direction = X | [optional] [default to False] |
| snake | bool | Flip fast direction for every second row | [optional] [default to False] |
Example
from jfjoch_client.models.grid_scan import GridScan
# TODO update the JSON string below
json = "{}"
# create an instance of GridScan from a JSON string
grid_scan_instance = GridScan.from_json(json)
# print the JSON string representation of the object
print(GridScan.to_json())
# convert the object into a dict
grid_scan_dict = grid_scan_instance.to_dict()
# create an instance of GridScan from a dict
grid_scan_from_dict = GridScan.from_dict(grid_scan_dict)