h5yaml 0.0.4__tar.gz → 0.0.5__tar.gz

{h5yaml-0.0.4 → h5yaml-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5yaml
-Version: 0.0.4
+Version: 0.0.5
 Summary: Use YAML configuration file to generate HDF5/netCDF4 formated files.
 Project-URL: Homepage, https://github.com/rmvanhees/h5_yaml
 Project-URL: Source, https://github.com/rmvanhees/h5_yaml

h5yaml-0.0.5/src/h5yaml/Data/h5_testing.yaml

@@ -0,0 +1,103 @@
+# YAML
+#
+# Configuration file to test the implementation of classes H5Yaml and NcYaml
+#
+# This file is part of h5_yaml:
+#    https://github.com/rmvanhees/h5_yaml.git
+#
+# Copyright (c) 2025 SRON
+#    All Rights Reserved
+#
+# License:  BSD-3-Clause
+#
+# Define groups
+groups:
+  - group_00
+  - group_01
+  - group_02
+
+# Define dimensions
+# Note dimensions with an attribute 'long_name' will also be generated as variable
+dimensions:
+  number_of_images:
+    _dtype: u2
+    _size: 0
+  samples_per_image:
+    _dtype: u4
+    _size: 203500
+  column:
+    _dtype: u2
+    _size: 640
+  row:
+    _dtype: u2
+    _size: 512
+  time:
+    _dtype: f8
+    _size: 0
+    _FillValue: -32767
+    long_name: Attitude sample time (seconds of day)
+    calendar: proleptic_gregorian
+    units: seconds since %Y-%m-%d %H:%M:%S
+    valid_min: 0
+    valid_max: 92400
+
+# Define compound types
+# - compound elements must have a data-type, and can have a unit and long_name 
+compounds:
+  stats_dtype:
+    time: [u8, seconds since 1970-01-01T00:00:00, timestamp]
+    index: [u2, '1', index]
+    tbl_id: [u1, '1', binning id]
+    saa: [u1, '1', saa-flag]
+    coad: [u1, '1', co-addings]
+    texp: [f4, ms, exposure time]
+    lat: [f4, degree, latitude]
+    lon: [f4, degree, longitude]
+    avg: [f4, '1', '$S - S_{ref}$']
+    unc: [f4, '1', '\u03c3($S - S_{ref}$)']
+    dark_offs: [f4, '1', dark-offset]
+
+  geo_dtype:
+    lat: [f4, latitude]
+    lon: [f4, longitude]
+    
+# Define variables
+variables:
+  /group_00/detector_images:
+    _dtype: u2
+    _dims: [number_of_images, column, row]
+    _FillValue: 65535
+    long_name: Detector pixel values
+    comment: unbinned full-frame data
+    units: '1'
+    valid_min: 0
+    valid_max: 65534
+  /group_01/detector_images:
+    _dtype: u2
+    _dims: [number_of_images, samples_per_image]
+    _FillValue: 65535
+    _compression: 1
+    long_name: Detector pixel values
+    comment: variable binned data (filled to the largest samples_per_image)
+    units: '1'
+    valid_min: 0
+    valid_max: 65534
+  /group_01/stats:
+    _dtype: stats_dtype
+    _dims: [time]
+    comment: detector map statistics
+  /group_02/detector_images:
+    _dtype: u2
+    _dims: [number_of_images]
+    _vlen: True
+    _FillValue: 65535
+    long_name: Detector pixel values
+    comment: variable binned (vlen) data
+    units: '1'
+    valid_min: 0
+    valid_max: 65534
+  /group_02/stats:
+    _dtype: stats_dtype
+    _vlen: True
+    _dims: [time]
+    comment: detector map statistics (vlen)

h5yaml-0.0.4/src/h5yaml/Data/h5_testing.yaml → h5yaml-0.0.5/src/h5yaml/Data/nc_testing.yaml

@@ -57,10 +57,6 @@ compounds:
     unc: [f4, '1', '\u03c3($S - S_{ref}$)']
     dark_offs: [f4, '1', dark-offset]
 
-  geo_dtype:
-    lat: [f4, latitude]
-    lon: [f4, longitude]
-    
 # Define variables
 variables:
   /group_00/detector_images:
@@ -84,7 +80,6 @@ variables:
     valid_max: 65534
   /group_01/stats:
     _dtype: stats_dtype
-    _vlen: True
     _dims: [time]
     comment: detector map statistics
   /group_02/detector_images:

h5yaml-0.0.4/src/h5yaml/yaml_h5py.py → h5yaml-0.0.5/src/h5yaml/yaml_h5.py

@@ -236,7 +236,14 @@ class H5Yaml:
                     shuffle = True
 
                 if val.get("_vlen"):
-                    ds_dtype = h5py.vlen_dtype(ds_dtype)
+                    ds_name = (
+                        val["_dtype"].split("_")[0]
+                        if "_" in val["_dtype"]
+                        else val["_dtype"]
+                    ) + "_vlen"
+                    if ds_name not in fid:
+                        fid[ds_name] = h5py.vlen_dtype(ds_dtype)
+                    ds_dtype = fid[ds_name]
                     fillvalue = None
                     if ds_maxshape == (None,):
                         ds_chunk = (16,)

{h5yaml-0.0.4 → h5yaml-0.0.5}/src/h5yaml/yaml_nc.py

@@ -258,7 +258,7 @@ class NcYaml:
 def tests() -> None:
     """..."""
     print("Calling NcYaml")
-    NcYaml(files("h5yaml.Data") / "h5_testing.yaml").create("test_yaml.nc")
+    NcYaml(files("h5yaml.Data") / "nc_testing.yaml").create("test_yaml.nc")
 
 
 if __name__ == "__main__":