Libgdal breaks read_gdal_vrt from readfile.py

[mthsdiniz-usp]

Description of the problem

When installing libgdal-netcdf / libgdal-hdf5 on the environment and trying to execute !smallbaselineApp.py, it fails when trying to load_data.

When import readfile from mintpy.utils and trying to read the same file, it works without any issues:

from mintpy.utils import readfile
fname = '/home/sagemaker-user/displacement/MintPy/data/lafayette/data/S1_038899_IW3_20170111_20170123_VV_INT40_73F7/S1_038899_IW3_20170111_20170123_VV_INT40_73F7_unw_phase_clipped.tif'
readfile.read_gdal_vrt(fname)

My environment has multiples packages because i'm working of Sagemaker JupyterLab and run multiple different packages in the same kernel.

Full script that generated the error

!smallbaselineApp.py --dir {work_dir} {mintpy_config} --dostep load_data

Full error message

MintPy version 1.6.1, date 2024-07-31
--RUN-at-2025-02-06 16:55:50.732085--
Current directory: /home/sagemaker-user/displacement/MintPy/notebooks
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: /home/sagemaker-user/displacement/MintPy/data/lafayette
read custom template file: /home/sagemaker-user/displacement/MintPy/data/lafayette/mintpy_config.txt
update default template based on input custom template
No new option value found, skip updating /home/sagemaker-user/displacement/MintPy/data/lafayette/smallbaselineApp.cfg
read default template file: /home/sagemaker-user/displacement/MintPy/data/lafayette/smallbaselineApp.cfg


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

load_data.py --template /home/sagemaker-user/displacement/MintPy/data/lafayette/smallbaselineApp.cfg /home/sagemaker-user/displacement/MintPy/data/lafayette/mintpy_config.txt --project mintpy_config
processor : hyp3
SAR platform/sensor : unknown from project name "mintpy_config"
--------------------------------------------------
prepare metadata files for hyp3 products
prep_hyp3.py "/home/sagemaker-user/displacement/MintPy/data/lafayette/data/*/*_unw_phase_clipped.tif"
/opt/conda/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(
ERROR 4: `/home/sagemaker-user/displacement/MintPy/data/lafayette/data/S1_038899_IW3_20170111_20170123_VV_INT40_73F7/S1_038899_IW3_20170111_20170123_VV_INT40_73F7_unw_phase_clipped.tif' not recognized as being in a supported file format.
Traceback (most recent call last):
  File "/opt/conda/bin/smallbaselineApp.py", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mintpy/cli/smallbaselineApp.py", line 209, in main
    run_smallbaselineApp(inps)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/smallbaselineApp.py", line 1155, in run_smallbaselineApp
    app.run(steps=inps.runSteps)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/smallbaselineApp.py", line 908, in run
    self.run_load_data(sname)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/smallbaselineApp.py", line 176, in run_load_data
    mintpy.cli.load_data.main(iargs)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/cli/load_data.py", line 123, in main
    load_data(inps)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/load_data.py", line 812, in load_data
    prepare_metadata(iDict)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/load_data.py", line 636, in prepare_metadata
    prep_module.main(iargs)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/cli/prep_hyp3.py", line 94, in main
    prep_hyp3(inps)
  File "/opt/conda/lib/python3.11/site-packages/mintpy/prep_hyp3.py", line 163, in prep_hyp3
    meta = readfile.read_gdal_vrt(fname)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mintpy/utils/readfile.py", line 1701, in read_gdal_vrt
    atr['WIDTH']  = ds.RasterXSize
                    ^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'RasterXSize'

System information

• Operating system:
• Python environment: micromamba + pip (txt file attached)

base_micromamba.txt
base_pip.txt

• MintPy version: 1.6.1
• InSAR processor/product: isce2
• Your custom / default template file (if the bug is related to a specific dataset):

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[codeautopilot]

Potential solution

The bug is likely caused by an issue with the GDAL library configuration or installation, which prevents it from recognizing certain file formats. The solution involves ensuring that GDAL is correctly installed with all necessary drivers and that the environment is properly configured to handle the file formats used by MintPy. Additionally, implementing error handling and logging can help diagnose and resolve the issue more effectively.

What is causing this bug?

The bug is caused by the GDAL library not recognizing the file format of the input file, leading to a NoneType object being returned by gdal.Open. This results in an AttributeError when the code attempts to access attributes like RasterXSize. The root causes could be:

1. Missing GDAL Drivers: The GDAL installation might lack the necessary drivers to support the file format, such as NetCDF or HDF5.
2. Incorrect GDAL Installation: The GDAL library might not be installed correctly, or there might be a version mismatch between the GDAL library and its Python bindings.
3. File Path Issues: The file path provided to read_gdal_vrt might be incorrect or the file might not be accessible.
4. Environment Configuration: The environment might not be set up correctly, with missing environment variables or conflicting packages.

Code

To address the issue, the following steps and code modifications are recommended:

1. Verify GDAL Installation: Ensure GDAL is installed with the necessary drivers. You can check the supported formats using:

   gdalinfo --formats

2. Specify GDAL in requirements.txt: Add GDAL with a specific version to the requirements.txt file to ensure compatibility:

   gdal==3.4.1
   

3. Handle None Return in read_gdal_vrt: Modify the read_gdal_vrt function to handle cases where gdal.Open returns None:

   from osgeo import gdal
   
   def read_gdal_vrt(fname):
       ds = gdal.Open(fname)
       if ds is None:
           raise RuntimeError(f"GDAL could not open the file: {fname}. Check if the file format is supported and the file path is correct.")
       
       atr = {}
       atr['WIDTH'] = ds.RasterXSize
       atr['LENGTH'] = ds.RasterYSize
       # Additional attribute extraction...
       return atr

4. Enable GDAL Exceptions: Use GDAL's exception handling to get more informative error messages:

   gdal.UseExceptions()

5. Check File Path: Before calling read_gdal_vrt, ensure the file path is valid and the file is accessible:

   import os
   
   if not os.path.exists(fname):
       raise FileNotFoundError(f"The file {fname} does not exist.")

How to replicate the bug

1. Set up an environment with MintPy and install the necessary dependencies, but omit the GDAL library or install an incompatible version.
2. Attempt to run the smallbaselineApp.py script with the --dostep load_data option.
3. Ensure the input file is in a format that requires specific GDAL drivers (e.g., NetCDF or HDF5) that are not installed.
4. Observe the error message indicating that the file format is not recognized and the AttributeError due to a NoneType object.

By following these steps, you should be able to replicate the bug and verify the effectiveness of the proposed solution.

Click here to create a Pull Request with the proposed solution

Files used for this task:

Changes on requirements.txt

Analysis Report

Overview

The requirements.txt file lists the Python packages and their versions required for the project. The issue reported involves a problem with the read_gdal_vrt function from the readfile.py module, which is related to GDAL (Geospatial Data Abstraction Library). The error message indicates that a file is not recognized as being in a supported format, and an AttributeError occurs because a NoneType object is being accessed.

Potential Causes of the Bug

1. GDAL Version Compatibility: The requirements.txt file does not explicitly list GDAL or its version. If GDAL is not specified, it might lead to compatibility issues, especially if the environment has multiple packages that could conflict with GDAL's operation.

2. Missing GDAL in Requirements: The absence of GDAL in the requirements.txt file means that its installation and version management are not controlled, which can lead to unexpected behavior if the wrong version is installed.

3. Dependency Conflicts: Other packages in the environment might have dependencies that conflict with GDAL, leading to issues in file recognition and processing.

Recommendations

1. Specify GDAL in requirements.txt: Add GDAL to the requirements.txt file with a specific version that is known to be compatible with the rest of the environment and the MintPy version being used. This will help ensure that the correct version is installed.

2. Check GDAL Installation: Verify that GDAL is correctly installed in the environment. This can be done by running gdalinfo --version in the terminal to check the installed version.

3. Environment Isolation: Consider using a virtual environment or a container to isolate dependencies and avoid conflicts with other packages installed in the system.

4. Review GDAL Configuration: Ensure that GDAL is configured correctly in the environment. This includes setting any necessary environment variables that GDAL might require.

By addressing these points, the issue with the read_gdal_vrt function not recognizing the file format should be mitigated.

Changes on src/mintpy/cli/smallbaselineApp.py

Analysis of src/mintpy/cli/smallbaselineApp.py

Overview

The script smallbaselineApp.py is a command-line interface for running a routine time series analysis for Small Baseline InSAR Stack using MintPy. It handles command-line arguments, sets up the environment, and calls the main processing function run_smallbaselineApp.

Key Functions

• create_parser: Sets up the command-line argument parser with various options for running the application.
• cmd_line_parse: Parses command-line arguments and performs checks on the input templates and options.
• read_inps2run_steps: Determines which processing steps to run based on the input arguments.
• main: The main entry point that parses arguments and calls the run_smallbaselineApp function.

Relevant Sections for the Bug

The issue reported involves the read_gdal_vrt function from readfile.py, which is called indirectly through the run_smallbaselineApp function. The error suggests that the GDAL library is not recognizing the file format, leading to a NoneType object error when accessing RasterXSize.

Potential Causes of the Bug

1. File Path Handling: Ensure that the file path passed to read_gdal_vrt is correct and accessible. The script should verify the existence of the file before attempting to read it.
2. GDAL Configuration: The environment might not be correctly configured to handle the file format. This could be due to missing drivers or incorrect GDAL settings.
3. Environment Variables: Check if any necessary environment variables for GDAL are set before calling the function. This includes paths to GDAL data or configuration files.
4. Error Handling: The script should handle cases where read_gdal_vrt returns None gracefully, possibly by logging an error message or attempting a fallback.

Recommendations

• Verify File Path: Add checks to ensure the file path is valid and the file is accessible before calling read_gdal_vrt.
• GDAL Setup: Ensure that GDAL is correctly configured in the environment. This might involve setting environment variables or ensuring the correct version of GDAL is installed.
• Error Handling: Implement error handling around the call to read_gdal_vrt to catch and log any issues with file reading.
• Logging: Add logging to capture the state of the environment and any relevant configuration details when the error occurs.

Conclusion

The script itself does not directly manipulate the GDAL configuration or file paths, but it is crucial to ensure that the environment is correctly set up before running the application. The issue likely lies in the environment configuration or the handling of file paths and formats.

Changes on src/mintpy/utils/readfile.py

Analysis Report for readfile.py

Overview

The readfile.py file is a utility module in the MintPy project designed to handle various file reading operations, particularly for geospatial data formats. It includes functions to read metadata and data from different file types, including HDF5, binary, and GDAL-supported formats. The file also contains mappings for data type conversions between different geospatial data formats.

Relevant Function: read_gdal_vrt

The function read_gdal_vrt is responsible for reading metadata from GDAL VRT files. It uses the GDAL library to open and read the file, extracting attributes such as width, length, data type, and geotransformation details.

Potential Issues

1. GDAL Configuration: The error message indicates that the GDAL library might not be correctly configured to recognize the file format. This could be due to missing drivers or incorrect installation of GDAL.

2. File Path Handling: The function uses gdal.Open to open the file. If the file path is incorrect or the file is not accessible, gdal.Open will return None, leading to the AttributeError when trying to access ds.RasterXSize.

3. Unsupported File Format: The error message "not recognized as being in a supported file format" suggests that the file might not be in a format supported by the current GDAL installation. This could be due to missing drivers for specific formats like NetCDF or HDF5.

4. GDAL Version Compatibility: The function relies on GDAL's Python bindings. If there is a version mismatch between the installed GDAL library and its Python bindings, it might cause unexpected behavior.

Recommendations

• Verify GDAL Installation: Ensure that GDAL is correctly installed with all necessary drivers. This can be done by checking the output of gdalinfo --formats to see if the required formats are supported.

• Check File Path: Confirm that the file path provided to read_gdal_vrt is correct and that the file is accessible.

• Handle None Return: Add a check after gdal.Open to handle cases where it returns None, and provide a more informative error message.

• GDAL Exception Handling: Consider using gdal.UseExceptions() to enable exception handling in GDAL, which can provide more detailed error messages.

Conclusion

The read_gdal_vrt function is likely encountering issues due to GDAL configuration or file path problems. Addressing these areas should help resolve the bug reported by the user. Further investigation into the GDAL installation and environment setup is recommended to ensure compatibility and support for the required file formats.

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