hyp3 + mintpy: Error in Second Step (Modify Network)

[hariiirs]

Description of the problem

I did the following steps -

1. Downloaded unwrapped interferograms from ASF site (Hyp3 processed)
2. Unzipped each interferogram
3. Open jupyter notebook (mintpy was installed i a separate environment)
4. Defined directories
5. Clipped a common AOI with UTM projection
6. Generated mintpy_config.txt file with required parameters
7. Run first step i.e load_data (completed successfully)
8. Run second step (modify_network), then the following error message came

!smallbaselineApp.py --dir ./output ./output/mintpy_config.txt --dostep modify_network # each path is correct

Full script that generated the error

MintPy version 1.5.3, date 2023-11-23
--RUN-at-2024-01-24 14:32:44.038449--
Current directory: /home/iirs/joshimath/test
Run routine processing with smallbaselineApp.py on steps: ['modify_network']
Remaining steps: ['reference_point', 'quick_overview', 'correct_unwrap_error', 'invert_network', 'correct_LOD', 'correct_SET', 'correct_troposphere', 'deramp', 'correct_topography', 'residual_RMS', 'reference_date', 'velocity', 'geocode', 'google_earth', 'hdfeos5']
--------------------------------------------------
Project name: mintpy_config
Go to work directory: /home/iirs/joshimath/test/output
read custom template file: /home/iirs/joshimath/test/output/mintpy_config.txt
update default template based on input custom template
    mintpy.network.coherenceBased: yes --> auto
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: /home/iirs/joshimath/test/output/smallbaselineApp.cfg


******************** step - modify_network ********************
Input data seems to be geocoded. Lookup file not needed.
['/home/iirs/joshimath/test/output/waterMask.h5'] exists and is newer than ['/home/iirs/joshimath/test/output/inputs/geometryGeo.h5'] --> skip.

modify_network.py /home/iirs/joshimath/test/output/inputs/ifgramStack.h5 -t /home/iirs/joshimath/test/output/smallbaselineApp.cfg
read options from template file: smallbaselineApp.cfg
No lookup table (longitude or rangeCoord) found in files.
No input option found to remove interferogram
Keep all interferograms by enable --reset option
--------------------------------------------------
reset dataset 'dropIfgram' to True for all interferograms for file: /home/iirs/joshimath/test/output/inputs/ifgramStack.h5
touch coherenceSpatialAvg.txt

plot_network.py /home/iirs/joshimath/test/output/inputs/ifgramStack.h5 -t /home/iirs/joshimath/test/output/smallbaselineApp.cfg --nodisplay -d coherence -v 0.2 1.0
read options from template file: smallbaselineApp.cfg
read temporal/spatial baseline info from file: /home/iirs/joshimath/test/output/inputs/ifgramStack.h5
open ifgramStack file: ifgramStack.h5
['coherenceSpatialAvg.txt'] exists and is newer than ['/home/iirs/joshimath/test/output/waterMask.h5'] --> skip.
coherenceSpatialAvg.txt already exists, read it directly
number of acquisitions: 111
number of interferograms: 416
shift all perp baseline by -71.0221176147461 to zero mean for plotting
--------------------------------------------------
number of interferograms marked as drop: 0
number of interferograms marked as keep: 416
number of acquisitions marked as drop: 0
Traceback (most recent call last):
  File "/home/iirs/miniconda3/envs/mint/bin/smallbaselineApp.py", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/iirs/miniconda3/envs/mint/lib/python3.11/site-packages/mintpy/cli/smallbaselineApp.py", line 208, in main
    run_smallbaselineApp(inps)
  File "/home/iirs/miniconda3/envs/mint/lib/python3.11/site-packages/mintpy/smallbaselineApp.py", line 1117, in run_smallbaselineApp
    app.run(steps=inps.runSteps)
  File "/home/iirs/miniconda3/envs/mint/lib/python3.11/site-packages/mintpy/smallbaselineApp.py", line 877, in run
    self.run_network_modification(sname)
  File "/home/iirs/miniconda3/envs/mint/lib/python3.11/site-packages/mintpy/smallbaselineApp.py", line 258, in run_network_modification
    mintpy.cli.plot_network.main(iargs)
  File "/home/iirs/miniconda3/envs/mint/lib/python3.11/site-packages/mintpy/cli/plot_network.py", line 170, in main
    plot_network(inps)
  File "/home/iirs/miniconda3/envs/mint/lib/python3.11/site-packages/mintpy/plot_network.py", line 148, in plot_network
    inps = read_network_info(inps)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/iirs/miniconda3/envs/mint/lib/python3.11/site-packages/mintpy/plot_network.py", line 107, in read_network_info
    raise ValueError(msg)
ValueError: Invalid NaN value found in the following kept pairs for Bperp or coherence! 
	They likely have issues, check them and maybe exclude them in your network.
	['20190505_20190610', '20190610_20190704', '20190610_20190716', '20190610_20190728', '20190704_20190716', '20190704_20190728', '20190704_20190821', '20190716_20190728', '20190716_20190821', '20190716_20190827', '20190728_20190821', '20190728_20190827', '20190728_20190908', '20190821_20190827', '20190821_20190908', '20190821_20190920', '20190821_20191002', '20190827_20190908', '20190827_20190920', '20190827_20191002', '20190827_20191014', '20190908_20190920', '20190908_20191002', '20190908_20191014', '20190908_20191026', '20190920_20191002', '20190920_20191014', '20190920_20191026', '20190920_20191107', '20191002_20191014', '20191002_20191026', '20191002_20191107', '20191002_20191119', '20191014_20191026', '20191014_20191107', '20191014_20191119', '20191014_20191201', '20191026_20191107', '20191026_20191119', '20191026_20191201', '20191026_20191213', '20191107_20191119', '20191107_20191201', '20191107_20191213', '20191107_20191219', '20191107_20191225', '20191119_20191201', '20191119_20191213', '20191119_20191219', '20191119_20191225', '20191119_20200106', '20191201_20191213', '20191201_20191219', '20191201_20191225', '20191201_20200106', '20191201_20200112', '20191201_20200118', '20191213_20191219', '20191213_20191225', '20191213_20200106', '20191213_20200112', '20191213_20200118', '20191213_20200124', '20191219_20191225', '20191219_20200106', '20191219_20200112', '20191219_20200118', '20191219_20200124', '20191225_20200106', '20191225_20200112', '20191225_20200118', '20191225_20200124', '20200106_20200112', '20200106_20200118', '20200106_20200124', '20200112_20200118', '20200112_20200124', '20200118_20200124', '20200118_20200312', '20200124_20200312', '20200124_20200324', '20200312_20200324', '20200312_20200405', '20200312_20200417', '20200312_20200429', '20200324_20200405', '20200324_20200417', '20200324_20200429', '20200324_20200511', '20200405_20200417', '20200405_20200429', '20200405_20200511', '20200405_20200523', '20200417_20200429', '20200417_20200511', '20200417_20200523', '20200417_20200604', '20200429_20200511', '20200429_20200523', '20200429_20200604', '20200429_20200616', '20200511_20200523', '20200511_20200604', '20200511_20200616', '20200511_20200628', '20200523_20200604', '20200523_20200616', '20200523_20200628', '20200523_20200710', '20200604_20200616', '20200604_20200628', '20200604_20200710', '20200604_20200722', '20200616_20200628', '20200616_20200710', '20200616_20200722', '20200616_20200803', '20200628_20200710', '20200628_20200722', '20200628_20200803', '20200628_20200815', '20200710_20200722', '20200710_20200803', '20200710_20200815', '20200710_20200827', '20200722_20200803', '20200722_20200815', '20200722_20200827', '20200722_20200908', '20200803_20200815', '20200803_20200827', '20200803_20200908', '20200803_20200920', '20200815_20200827', '20200815_20200908', '20200815_20200920', '20200815_20201002', '20200827_20200908', '20200827_20200920', '20200827_20201002', '20200827_20201014', '20200908_20200920', '20200908_20201002', '20200908_20201014', '20200908_20201026', '20200920_20201002', '20200920_20201014', '20200920_20201026', '20200920_20201107', '20201002_20201014', '20201002_20201026', '20201002_20201107', '20201002_20201119', '20201014_20201026', '20201014_20201107', '20201014_20201119', '20201014_20201201', '20201026_20201107', '20201026_20201119', '20201026_20201201', '20201026_20201213', '20201107_20201119', '20201107_20201201', '20201107_20201213', '20201107_20201225', '20201119_20201201', '20201119_20201213', '20201119_20201225', '20201119_20210106', '20201201_20201213', '20201201_20201225', '20201201_20210106', '20201201_20210118', '20201213_20201225', '20201213_20210106', '20201213_20210118', '20201213_20210130', '20201225_20210106', '20201225_20210118', '20201225_20210130', '20201225_20210211', '20210106_20210118', '20210106_20210130', '20210106_20210211', '20210106_20210217', '20210106_20210223', '20210118_20210130', '20210118_20210211', '20210118_20210217', '20210118_20210223', '20210118_20210307', '20210130_20210211', '20210130_20210217', '20210130_20210223', '20210130_20210307', '20210130_20210319', '20210211_20210217', '20210211_20210223', '20210211_20210307', '20210211_20210319', '20210211_20210331', '20210217_20210223', '20210217_20210307', '20210217_20210319', '20210217_20210331', '20210223_20210307', '20210223_20210319', '20210223_20210331', '20210223_20210412', '20210307_20210319', '20210307_20210331', '20210307_20210412', '20210307_20210424', '20210319_20210331', '20210319_20210412', '20210319_20210424', '20210319_20210506', '20210331_20210412', '20210331_20210424', '20210331_20210506', '20210331_20210518', '20210412_20210424', '20210412_20210506', '20210412_20210518', '20210412_20210530', '20210424_20210506', '20210424_20210518', '20210424_20210530', '20210424_20210611', '20210506_20210518', '20210506_20210530', '20210506_20210611', '20210506_20210623', '20210518_20210530', '20210518_20210611', '20210518_20210623', '20210518_20210705', '20210530_20210611', '20210530_20210623', '20210530_20210705', '20210530_20210717', '20210611_20210623', '20210611_20210705', '20210611_20210717', '20210611_20210729', '20210623_20210705', '20210623_20210717', '20210623_20210729', '20210623_20210810', '20210705_20210717', '20210705_20210729', '20210705_20210810', '20210705_20210822', '20210717_20210729', '20210717_20210810', '20210717_20210822', '20210717_20210903', '20210729_20210810', '20210729_20210822', '20210729_20210903', '20210729_20210915', '20210810_20210822', '20210810_20210903', '20210810_20210915', '20210810_20210927', '20210822_20210903', '20210822_20210915', '20210822_20210927', '20210822_20211009', '20210903_20210915', '20210903_20210927', '20210903_20211009', '20210903_20211021', '20210915_20210927', '20210915_20211009', '20210915_20211021', '20210915_20211102', '20210927_20211009', '20210927_20211021', '20210927_20211102', '20210927_20211114', '20211009_20211021', '20211009_20211102', '20211009_20211114', '20211009_20211126', '20211021_20211102', '20211021_20211114', '20211021_20211126', '20211021_20211208', '20211102_20211114', '20211102_20211126', '20211102_20211208', '20211102_20211220', '20211114_20211126', '20211114_20211208', '20211114_20211220', '20211114_20220101', '20211126_20211208', '20211126_20211220', '20211126_20220101', '20211126_20220113', '20211208_20211220', '20211208_20220101', '20211208_20220113', '20211220_20220101', '20211220_20220113', '20211220_20220206', '20220101_20220113', '20220101_20220206', '20220101_20220218', '20220113_20220206', '20220113_20220218', '20220206_20220218', '20220206_20220314', '20220206_20220326', '20220218_20220314', '20220218_20220326', '20220218_20220407', '20220314_20220326', '20220314_20220407', '20220314_20220419', '20220314_20220501', '20220326_20220407', '20220326_20220419', '20220326_20220501', '20220326_20220513', '20220407_20220419', '20220407_20220501', '20220407_20220513', '20220407_20220525', '20220419_20220501', '20220419_20220513', '20220419_20220525', '20220419_20220606', '20220501_20220513', '20220501_20220525', '20220501_20220606', '20220501_20220618', '20220513_20220525', '20220513_20220606', '20220513_20220618', '20220513_20220630', '20220525_20220606', '20220525_20220618', '20220525_20220630', '20220525_20220712', '20220606_20220618', '20220606_20220630', '20220606_20220712', '20220606_20220724', '20220618_20220630', '20220618_20220712', '20220618_20220724', '20220618_20220805', '20220630_20220712', '20220630_20220724', '20220630_20220805', '20220630_20220817', '20220712_20220724', '20220712_20220805', '20220712_20220817', '20220712_20220829', '20220724_20220805', '20220724_20220817', '20220724_20220829', '20220724_20220910', '20220805_20220817', '20220805_20220829', '20220805_20220910', '20220817_20220829', '20220817_20220910', '20220817_20221004', '20220829_20220910', '20220829_20221004', '20220829_20221016', '20220910_20221004', '20220910_20221016', '20220910_20221028', '20221004_20221016', '20221004_20221028', '20221004_20221109', '20221004_20221121', '20221016_20221028', '20221016_20221109', '20221016_20221121', '20221016_20221203', '20221028_20221109', '20221028_20221121', '20221028_20221203', '20221028_20221215', '20221109_20221121', '20221109_20221203', '20221109_20221215', '20221109_20221227', '20221121_20221203', '20221121_20221215', '20221121_20221227', '20221121_20230108', '20221203_20221215', '20221203_20221227', '20221203_20230108', '20221215_20221227', '20221215_20230108', '20221215_20230201', '20221227_20230108', '20221227_20230201', '20221227_20230213', '20230108_20230201', '20230108_20230213', '20230108_20230225', '20230201_20230213', '20230201_20230225', '20230201_20230426', '20230213_20230225', '20230213_20230426', '20230225_20230426']

Full error message

PASTE ERROR MESSAGE HERE

System information

• Operating system:
• Python environment:
• MintPy version:
• InSAR processor/product:
• Your custom / default template file (if the bug is related to a specific dataset):

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