Merge pull request #285 from markspec/284_sparsity_check_override

Author: tasansal

src/mdio/converters/exceptions.py

@@ -15,3 +15,16 @@ def __init__(self, grid_traces, segy_traces):
         )
 
         super().__init__(self.message)
+
+
+class GridTraceSparsityError(Exception):
+    """Raised when mdio grid will be sparsely populated from SEG-Y traces."""
+
+    def __init__(self, shape, num_traces):
+        """Initialize error."""
+        self.message = (
+            f"Grid shape: {shape} but SEG-Y tracecount: {num_traces}. "
+            "This grid is very sparse and most likely user error with indexing."
+        )
+
+        super().__init__(self.message)

src/mdio/converters/segy.py

@@ -4,6 +4,7 @@
 from __future__ import annotations
 
 import logging
+import os
 from datetime import datetime
 from datetime import timezone
 from importlib import metadata
@@ -16,6 +17,7 @@
 
 from mdio.api.io_utils import process_url
 from mdio.converters.exceptions import GridTraceCountError
+from mdio.converters.exceptions import GridTraceSparsityError
 from mdio.core import Grid
 from mdio.core.utils_write import write_attribute
 from mdio.segy import blocked_io
@@ -61,14 +63,16 @@ def grid_density_qc(grid: Grid, num_traces: int) -> None:
     Basic qc of the grid to check density and provide warning/exception
     when indexing is problematic to provide user with insights to the use.
     If trace density on the specified grid is less than 50% a warning is
-    logged.  If denisty is less than 1% an exception is raised.
+    logged.  If density is less than 10% an exception is raised. To ignore
+    trace sparsity check set environment variable:
+        MDIO_IGNORE_CHECKS = True
 
     Args:
         grid: The grid instance to check.
         num_traces: Expected number of traces.
 
     Raises:
-        GridTraceCountError: When the grid is too sparse.
+        GridTraceSparsityError: When the grid is too sparse.
     """
     grid_traces = np.prod(grid.shape[:-1], dtype=np.uint64)  # Exclude sample
     dims = {k: v for k, v in zip(grid.dim_names, grid.shape)}  # noqa: B905
@@ -78,16 +82,16 @@ def grid_density_qc(grid: Grid, num_traces: int) -> None:
 
     # Extreme case where the grid is very sparse (usually user error)
     if grid_traces > 10 * num_traces:
+        logger.warning("WARNING: Sparse mdio grid detected!")
         for dim_name in grid.dim_names:
             dim_min = grid.get_min(dim_name)
             dim_max = grid.get_max(dim_name)
             logger.warning(f"{dim_name} min: {dim_min} max: {dim_max}")
-
-        msg = (
-            f"Grid shape: {grid.shape} but SEG-Y tracecount: {num_traces}. "
-            "This grid is very sparse and most likely user error with indexing."
-        )
-        raise GridTraceCountError(msg)
+        if os.getenv("MDIO_IGNORE_CHECKS", False):
+            # Do not raise an exception if MDIO_IGNORE_CHECK is False
+            pass
+        else:
+            raise GridTraceSparsityError(grid.shape, num_traces)
 
     # Warning if we have above 50% sparsity.
     if grid_traces > 2 * num_traces: