Stitching scans...

[jonwright]

Assuming we do this using a masterfile full of links we need to patch the import imagefiles command to put in links with respect to frames.file.filename rather than the existing relative links.

Kind of a sad recipe. Otherwise I guess dataset would need to handle multiple masterfiles.

In raw data created a new dataset which has links to the existing one:

f1 = "/data/visitor/ma7058/id11/20260306/RAW_DATA/BFOconeNscope/BFOconeNscope_s3DXRD_z100/BFOconeNscope_s3DXRD_z100.h5"
s1 = list(range(1,203))
f2 = "/data/visitor/ma7058/id11/20260306/RAW_DATA/BFOconeNscope/BFOconeNscope_s3DXRD_z100_0003/BFOconeNscope_s3DXRD_z100_0003.h5"
s2 = list(range(2,101))

with h5py.File('BFOconeNscope_s3DXRD_merge.h5','w', track_order=True) as hout:
    for s in s1:
        for j in 1,2:
            scan = f'{s}.{j}'
            print(s,j,scan)
            hout[ scan ] = h5py.ExternalLink(f1, scan)
    for s in s2:
        for j in 1,2:
            scan = f'{s}.{j}'
            scanout = f'{s + len(s1) -1}.{j}'
            print(scan,scanout)
            hout[ scanout ] = h5py.ExternalLink(f2, scan)

Then when segmenting proceed as normal to create the dataset. Then patch the imagefiles code:

def import_imagefiles(self):
        """Get the Lima file names from the bliss master file, also scan_npoints"""
        # self.import_scans() should always be called before this function, so we know the detector
        self.imagefiles = []
        self.frames_per_file = []
        with h5py.File(self.masterfile, "r") as hin:
            bad = []
            for i, scan in enumerate(self.scans):
                if ("measurement" not in hin[scan]) or (
                    self.detector not in hin[scan]["measurement"]
                ):
                    print("Bad scan", scan)
                    bad.append(scan)
                    continue
                frames = hin[scan]["measurement"][self.detector]
                self.imageshape = frames.shape[1:]
                path = os.path.dirname(frames.file.filename)
                for vsrc in frames.virtual_sources():
                    self.imagefiles.append(os.path.join( path, vsrc.file_name))
                    self.frames_per_file.append(
                        vsrc.src_space.shape[0]
                    )  # not sure about this
                    # check limapath
                    if self.limapath is None:
                        self.limapath = vsrc.dset_name
                    assert self.limapath == vsrc.dset_name
        self.frames_per_file = np.array(self.frames_per_file, int)
        self.sparsefiles = [
            os.path.join(
                "sparsefiles", f"scan{i+1}_eiger_0000_sparse.h5",
            )
            for i, name in enumerate(self.imagefiles)
        ]

I think the patches needed are just this thing for dataset image file import, and maybe something for building master files from bits of scans