diff --git a/pims/bioformats.py b/pims/bioformats.py index 95d21dc1..c2dfc197 100644 --- a/pims/bioformats.py +++ b/pims/bioformats.py @@ -309,8 +309,12 @@ class BioformatsReader(FramesSequenceND): """ @classmethod def class_exts(cls): - return {'lsm', 'ipl', 'dm3', 'seq', 'nd2', 'ics', 'ids', - 'ipw', 'tif', 'tiff', 'jpg', 'bmp', 'lif', 'lei'} + # List of supported bioformats filetypes is in bioformats_filetypes.txt + # https://docs.openmicroscopy.org/bio-formats/5.7.1/supported-formats.html + with open('bioformats_filetypes.txt') as f: + extensions = f.read().split('\n') + extensions = set([ext[1:] for ext in extensions if ext]) + return extensions class_priority = 2 propagate_attrs = ['frame_shape', 'pixel_type', 'metadata', diff --git a/pims/bioformats_filetypes.txt b/pims/bioformats_filetypes.txt new file mode 100644 index 00000000..f7ca55ad --- /dev/null +++ b/pims/bioformats_filetypes.txt @@ -0,0 +1,165 @@ +.1sc +.2fl +.acff +.afi +.afm +.aim +.al3d +.am +.amiramesh +.apl +.arf +.avi +.bin +.bip +.bmp +.btf +.c01 +.cfg +.ch5 +.cif +.cr2 +.crw +.csv +.cxd +.czi +.dat +.dcm +.dib +.dicom +.dm2 +.dm3 +.dm4 +.dti +.dv +.eps +.epsi +.exp +.fdf +.fff +.ffr +.fits +.flex +.fli +.frm +.gel +.gif +.grey +.hdf +.hdr +.hed +.his +.htd +.html +.hx +.i2i +.ics +.ids +.im3 +.img +.ims +.inr +.ipl +.ipm +.ipw +.jp2 +.jpg +.jpk +.jpx +.l2d +.labels +.lei +.lif +.liff +.lim +.lms +.lsm +.mdb +.mea +.mnc +.mng +.mod +.mov +.mrc +.mrw +.msr +.mtb +.mvd2 +.naf +.nd +.nd2 +.ndpi +.ndpis +.nef +.nhdr +.nii +.nii.gz +.nrrd +.obf +.obsep +.oib +.oif +.oir +.ome +.ome.btf +.ome.tf2 +.ome.tf8 +.ome.tif +.ome.tiff +.ome.xml +.par +.pbm +.pcoraw +.pcx +.pds +.pgm +.pic +.pict +.png +.pnl +.ppm +.pr3 +.ps +.psd +.r3d +.raw +.rec +.res +.scn +.sdt +.seq +.sif +.sld +.sm2 +.sm3 +.spc +.spe +.spi +.stk +.stp +.svs +.sxm +.tf2 +.tf8 +.tfr +.tga +.tif +.tiff +.tnb +.top +.txt +.v +.vms +.vsi +.vws +.wat +.wlz +.xdce +.xml +.xqd +.xqf +.xv +.xys +.zfp +.zfr +.zvi