thyra 2.0.2__tar.gz → 2.0.3__tar.gz

{thyra-2.0.2 → thyra-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: thyra
-Version: 2.0.2
+Version: 2.0.3
 Summary: A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics
 License: MIT
 License-File: LICENSE

{thyra-2.0.2 → thyra-2.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "thyra"
-version = "2.0.2"
+version = "2.0.3"
 description = "A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics"
 authors = ["Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>"]
 maintainers = ["Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>"]

{thyra-2.0.2 → thyra-2.0.3}/thyra/__init__.py

@@ -36,7 +36,7 @@ warnings.filterwarnings(
     category=FutureWarning,
 )
 
-__version__ = "2.0.2"
+__version__ = "2.0.3"
 
 # Import key components - avoid wildcard imports
 try:

{thyra-2.0.2 → thyra-2.0.3}/thyra/converters/spatialdata/streaming_converter.py

@@ -129,10 +129,21 @@ class StreamingSpatialDataConverter(BaseSpatialDataConverter):
         n_x, n_y, n_z = metadata.dimensions
         n_pixels = n_x * n_y * n_z
 
-        # Estimate number of m/z bins after resampling using the same
-        # resolution path the axis builder will use, so the gate against
-        # PCS_SIZE_THRESHOLD_GB sees the real bin count.
-        if self._resampling_config:
+        # Prefer the axis that was actually built. ``convert()`` runs
+        # ``_initialize_conversion()`` -- and so ``_setup_mass_axis()`` --
+        # before it asks which method to use, so by the time this gate is
+        # evaluated the real bin count is known and there is nothing to
+        # estimate. That matters most on the raw-axis path, where the
+        # fallback below assumes a 10 mDa spacing that the data need not
+        # have: a continuous file carrying 4,000 points over 250-1200 m/z
+        # was scored as though it had 95,000, and a processed file whose
+        # spectra share no m/z values was scored far too low, which routed
+        # the largest datasets to the method that holds the most in memory.
+        if self._common_mass_axis is not None:
+            n_mz_bins = len(self._common_mass_axis)
+        elif self._resampling_config:
+            # Same resolution path the axis builder will use, so the gate
+            # against PCS_SIZE_THRESHOLD_GB sees the real bin count.
             _, _, _, n_mz_bins = self._resolve_resampling_plan()
         else:
             min_mass, max_mass = metadata.mass_range