Couldn't run $ dolphin2mintpy got, 'TypeError: Object dtype dtype('O') has no native HDF5 equivalent'

[Karthi-Wolf]

I had tried to run $ dolphin2mintpy with my ISCE2 & Dolphin. I couldn't make it. Can you please give me solution for this?
I'm using Mintpy 1.6.3 & dolphin 0.42.5 (developer version).
(I had used the full file path while procesing, here I mentioned full path in shorter way using **/)

$ dolphin2mintpy prepare  --unw-dir **/dolphin/unwrapped --cor-dir **/dolphin/interferograms --baseline-dir **/baselines --ref-xml **/reference/IW2.xml --ref-date 20160716
20:16:46 [INFO] dolphin2mintpy.metadata: Parsed ISCE2 XML: wavelength=0.05546576, range_ps=2.329562114715323, starting_range=845521.1272493784, prf=486.48631029955294, pass=DESCENDING, heading=-167.4, center_line_utc=1339.133
20:16:46 [INFO] dolphin2mintpy.metadata: Loaded baselines for 1 dates from **/baselines (ref: 20160716)
20:16:47 [INFO] dolphin2mintpy.prepare: Detected geometry: RADAR — auto (non-identity geotransform but no projection (treated as radar)) (override with geometry_mode='radar' or 'geo' if incorrect)
20:16:47 [INFO] dolphin2mintpy.prepare: Processing 2421 files (geometry_mode=auto)...
20:17:06 [INFO] dolphin2mintpy.prepare: Complete: 2421 .rsc written, 0 errors.

Done: 2421 .rsc files written.

$ dolphin2mintpy generate-config --work-dir **/dolphin/mintpy_new --unw-dir **/dolphin/unwrapped --dem-file **/merged/geom_reference/hgt.rdr.full --inc-angle-file **/merged/geom_reference/los.rdr.full --az-angle-file **/merged/geom_reference/los.rdr.full --lookup-y-file **/merged/geom_reference/lon.rdr.full --lookup-x-file **/merged/geom_reference/lat.rdr.full --processor isce
20:18:53 [INFO] dolphin2mintpy.config: Generated MintPy config: **/dolphin/mintpy_new/mintpy_config.txt
Config written: **/dolphin/mintpy_new/mintpy_config.txt

Next step: smallbaselineApp.py mintpy_config.txt

$dolphin2mintpy info --unw-dir **/dolphin/unwrapped

--------------------------------------------------
  Dolphin Stack Information
--------------------------------------------------

  Unwrapped files:     807
  Coherence files:     0
  ConnComp files:      807

  Date range:          20160704 -> 20250822
  Unique dates:        271
  Interferogram pairs: 807

  Existing .rsc files: 1614

--------------------------------------------------

$ smallbaselineApp.py mintpy_config.txt --dostep load_data
MintPy version 1.6.3, date 2025-11-23
--RUN-at-2026-04-27 20:06:53.923724--
Current directory: **/dolphin/mintpy_new
Run routine processing with smallbaselineApp.py on steps: ['load_data']
Remaining steps: ['modify_network', 'reference_point', 'quick_overview', 'correct_unwrap_error', 'invert_network', 'correct_LOD', 'correct_SET', 'correct_ionosphere', 'correct_troposphere', 'deramp', 'correct_topography', 'residual_RMS', 'reference_date', 'velocity', 'geocode', 'google_earth', 'hdfeos5']
--------------------------------------------------
Project name: mintpy_config
Go to work directory: **/dolphin/mintpy_new
copy default template file /home/incois/karthi/tools/MintPy/src/mintpy/defaults/smallbaselineApp.cfg to work directory
read custom template file: **/dolphin/mintpy_new/mintpy_config.txt
update default template based on input custom template
    mintpy.load.processor: auto --> isce
    mintpy.load.autoPath: auto --> no
    mintpy.load.unwFile: auto --> **/dolphin/unwrapped/*.unw.tif
    mintpy.load.corFile: auto --> **/dolphin/unwrapped/*.cor.tif
    mintpy.load.connCompFile: auto --> **/dolphin/unwrapped/*.unw.conncomp.tif
    mintpy.load.demFile: auto --> **/merged/geom_reference/hgt.rdr.full
    mintpy.load.lookupYFile: auto --> **/merged/geom_reference/lon.rdr.full
    mintpy.load.lookupXFile: auto --> **/merged/geom_reference/lat.rdr.full
    mintpy.load.incAngleFile: auto --> **/merged/geom_reference/los.rdr.full
    mintpy.load.azAngleFile: auto --> **/merged/geom_reference/los.rdr.full
    mintpy.networkInversion.weightFunc: auto --> coherence
    mintpy.networkInversion.maskDataset: auto --> connectComponent
    mintpy.networkInversion.minTempCoh: auto --> 0.4
    mintpy.troposphericDelay.method: auto --> no
    mintpy.deramp: auto --> no
    mintpy.topographicResidual: auto --> yes
    mintpy.save.kmz: auto --> yes
    mintpy.save.hdfEos5: auto --> no
copy mintpy_config.txt    to inputs   directory for backup.
copy smallbaselineApp.cfg to inputs   directory for backup.
copy mintpy_config.txt    to pic      directory for backup.
copy smallbaselineApp.cfg to pic      directory for backup.
read default template file: **/dolphin/mintpy_new/smallbaselineApp.cfg


******************** step - load_data ********************

load_data.py --template **/dolphin/mintpy_new/smallbaselineApp.cfg **/dolphin/mintpy_new/mintpy_config.txt --project mintpy_config
processor : isce
SAR platform/sensor : unknown from project name "mintpy_config"
--------------------------------------------------
prepare metadata files for isce products
/home/incois/karthi/tools/MintPy/src/mintpy/load_data.py:670: UserWarning: No input metadata file found: auto
  warnings.warn('No input metadata file found: {}'.format(iDict['mintpy.load.metaFile']))
prep_isce.py -m auto -g **/merged/geom_reference -b auto -f "**/dolphin/unwrapped/*.unw.tif" --geom-files hgt.rdr.full lon.rdr.full lat.rdr.full los.rdr.full los.rdr.full
/home/incois/karthi/tools/MintPy/src/mintpy/load_data.py:708: UserWarning: prep_isce.py failed. Assuming its result exists and continue...
  warnings.warn('prep_isce.py failed. Assuming its result exists and continue...')
--------------------------------------------------
updateMode : True
compression: default
multilook x/ystep: 1/1
multilook method : nearest
/home/incois/karthi/miniconda3/envs/isce_mint/lib/python3.11/site-packages/osgeo/gdal.py:311: FutureWarning: Neither gdal.UseExceptions() nor gdal.DontUseExceptions() has been explicitly called. In GDAL 4.0, exceptions will be enabled by default.
  warnings.warn(
--------------------------------------------------
searching geometry files info
input data files:
height          : **/merged/geom_reference/hgt.rdr.full
latitude        : **/merged/geom_reference/lon.rdr.full
longitude       : **/merged/geom_reference/lat.rdr.full
incidenceAngle  : **/merged/geom_reference/los.rdr.full
azimuthAngle    : **/merged/geom_reference/los.rdr.full
--------------------------------------------------
create HDF5 file **/dolphin/mintpy_new/inputs/geometryGeo.h5 with w mode
create dataset /height             of <class 'numpy.float32'>   in size of (11365, 47696) with compression = lzf
create dataset /latitude           of <class 'numpy.float32'>   in size of (11365, 47696) with compression = lzf
create dataset /longitude          of <class 'numpy.float32'>   in size of (11365, 47696) with compression = lzf
create dataset /incidenceAngle     of <class 'numpy.float32'>   in size of (11365, 47696) with compression = lzf
create dataset /azimuthAngle       of <class 'numpy.float32'>   in size of (11365, 47696) with compression = lzf
Traceback (most recent call last):
  File "/home/incois/karthi/miniconda3/envs/isce_mint/bin/smallbaselineApp.py", line 6, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/incois/karthi/tools/MintPy/src/mintpy/cli/smallbaselineApp.py", line 209, in main
    run_smallbaselineApp(inps)
  File "/home/incois/karthi/tools/MintPy/src/mintpy/smallbaselineApp.py", line 1155, in run_smallbaselineApp
    app.run(steps=inps.runSteps)
  File "/home/incois/karthi/tools/MintPy/src/mintpy/smallbaselineApp.py", line 908, in run
    self.run_load_data(sname)
  File "/home/incois/karthi/tools/MintPy/src/mintpy/smallbaselineApp.py", line 176, in run_load_data
    mintpy.cli.load_data.main(iargs)
  File "/home/incois/karthi/tools/MintPy/src/mintpy/cli/load_data.py", line 121, in main
    load_data(inps)
  File "/home/incois/karthi/tools/MintPy/src/mintpy/load_data.py", line 841, in load_data
    geom_geo_obj.write2hdf5(
  File "/home/incois/karthi/tools/MintPy/src/mintpy/objects/stackDict.py", line 798, in write2hdf5
    f.attrs[key] = value
    ~~~~~~~^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/incois/karthi/miniconda3/envs/isce_mint/lib/python3.11/site-packages/h5py/_hl/attrs.py", line 104, in __setitem__
    self.create(name, data=value)
  File "/home/incois/karthi/miniconda3/envs/isce_mint/lib/python3.11/site-packages/h5py/_hl/attrs.py", line 182, in create
    htype = h5t.py_create(original_dtype, logical=True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/h5t.pyx", line 1658, in h5py.h5t.py_create
  File "h5py/h5t.pyx", line 1682, in h5py.h5t.py_create
  File "h5py/h5t.pyx", line 1742, in h5py.h5t.py_create
TypeError: Object dtype dtype('O') has no native HDF5 equivalent

[bcankara]

Hello! Thanks for reporting this.

This is a workflow/usage issue, not a bug in dolphin2mintpy itself, but it highlights a tricky edge case when mixing Dolphin GeoTIFFs with raw ISCE2 binary files.

What is happening?
The TypeError: Object dtype dtype('O') is a known MintPy crash. It happens because:

1. Your config uses processor = isce, so MintPy tries to run its prep_isce.py script.
2. prep_isce.py crashes early (UserWarning: prep_isce.py failed) because it expects ISCE-format interferograms, but you provided Dolphin .tif files.
3. Because it crashes, it fails to generate the required .vrt and .rsc metadata sidecars for your raw ISCE geometry files (hgt.rdr.full, etc.).
4. When MintPy attempts to read these raw geometry files without their metadata sidecars, some attributes return as None, causing h5py to crash.

Does dolphin2mintpy solve this?
Yes, our bridge is designed to completely bypass prep_isce.py by generating .rsc metadata sidecars for all files (including geometry). However, dolphin2mintpy prepare expects the geometry files to be GeoTIFFs, but you passed raw ISCE2 .full binaries directly to generate-config without passing them through the prepare step.

How to fix it:

Solution 1: Use GeoTIFF Geometry files (Recommended)
Dolphin can export geometry files as GeoTIFFs. If you use GeoTIFFs, dolphin2mintpy will handle everything smoothly.

1. Make sure you have your geometry files as .tif (e.g., hgt.tif, los.tif).
2. Run the prepare step again, and this time include the --geometry-dir argument pointing to those GeoTIFFs:

   dolphin2mintpy prepare --unw-dir **/dolphin/unwrapped --cor-dir **/dolphin/interferograms --baseline-dir **/baselines --geometry-dir **/path/to/geometry_tiffs --ref-xml **/reference/IW2.xml --ref-date 20160716

3. Generate your config pointing to these .tif files instead of the .full files.

Solution 2: Manually run prep_isce.py for geometry files (Quick Workaround)
If you must use the raw ISCE2 .full binaries, you need to manually prepare them before running MintPy. Run this in your terminal:

prep_isce.py -m auto -b auto -g **/merged/geom_reference --geom-files hgt.rdr.full lon.rdr.full lat.rdr.full los.rdr.full los.rdr.full

Once this successfully creates the .vrt files for your geometry, you can run smallbaselineApp.py mintpy_config.txt --dostep load_data without errors.