Merge branch 'developer' into main

.github/environment.yml

@@ -7,4 +7,5 @@ dependencies:
   - build
   - conda-build
   - conda-verify
+  - boa
   - numpy

.github/workflows/build_conda_pkgs.yml

@@ -23,7 +23,7 @@ jobs:
     - name: Build conda pkg
       shell: bash -l {0}
       run: |
-          conda build .
+          conda mambabuild .
     - name: Upload artifacts
       uses: actions/upload-artifact@v2
       with:

README.md

@@ -80,5 +80,5 @@ FILE_CONTENTS {
 We aim to follow NEP 29 regarding supported Python and Numpy versions https://numpy.org/neps/nep-0029-deprecation_policy.html#nep29
 
 At the moment this means:
-* Python 3.8-3.10
-* Numpy 1.19-1.21
+* Python 3.9-3.11
+* Numpy 1.22-1.24

conda-recepie/conda_build_config.yaml

@@ -9,6 +9,7 @@ python:
     - 3.11
     - 3.11
     - 3.11
+
 
 numpy: 
     - 1.20
@@ -22,7 +23,6 @@ numpy:
     - 1.25
     - 1.26
 
-
 zip_keys:
     - python
     - numpy

hdf5maker/__init__.py

@@ -1,5 +1,5 @@
 
-from .hdf5_file import write_data_file, write_master_file, get_output_fname, Hdf5File
+from .hdf5_file import write_data_file, write_master_file, get_output_fname, Hdf5File, write_simple_master_file
 from .io import read_bad_pixels, read_bad_channels
 
 #Imports related to raw files

hdf5maker/hdf5_file.py

@@ -58,10 +58,15 @@ def write_data_file(
     fname,
     data,
     image_nr_low=1,
-    compression=hdf5plugin.Bitshuffle(nelems=0, lz4=True),
+    compression=hdf5plugin.Bitshuffle(nelems=0, cname='lz4'),
 ):
     print(color.info(f"Writing: {fname}"))
-    f = h5py.File(fname, "w")
+    try:
+        f = h5py.File(fname, "w")
+    except Exception as inst:
+        print(color.error(f"Writing of: {fname} failed could not open file"))
+        raise inst
+
     nxentry, nxdata = create_entry_and_data(f)
     ds = nxdata.create_dataset(
         "data",
@@ -76,14 +81,24 @@ def write_data_file(
     ds.attrs["image_nr_high"] = np.int32(image_nr_low + data.shape[0] - 1)
     f.close()
 
+def write_simple_master_file(fname, data_files):
+    print(color.info(f"Writing: {fname}"))
+    f = h5py.File(fname, "w")
+    nxentry, nxdata = create_entry_and_data(f)
+
+    # Link written data sets:
+    for i, fname in enumerate(data_files, start=1):
+        f[f"entry/data/data_{i:06d}"] = h5py.ExternalLink(fname, "entry/data/data")
+
+    f.close()
 
 def write_master_file(
     fname,
     data_files,
     pixel_mask=None,
     raw_master_file = None,
     i0 = None,
-    compression=hdf5plugin.Bitshuffle(nelems=0, lz4=True),
+    compression=hdf5plugin.Bitshuffle(nelems=0, cname='lz4'),
 ):
     print(color.info(f"Writing: {fname}"))
     f = h5py.File(fname, "w")

hdf5maker/raw_file_reader.py

@@ -165,7 +165,13 @@ def __init__(self, fname, redistribute=None, lazy=False, fastquad=False):
                     self.redistribute = True
             self.dt = to_dtype(self.master["Dynamic Range"])
             self.dr = self.master["Dynamic Range"]
-            self.total_frames = self.master["Frames in File"]
+            #Look for the new field Frames in File and if this is not present
+            #fall back to Total Frames
+            try:
+                self.total_frames = self.master["Frames in File"]
+            except:
+                self.total_frames = self.master["Total Frames"]
+
             self.max_frames_per_file = self.master["Max Frames Per File"]
             self.file_geometry = self.master["Pixels"][::-1]
             self.frames_per_file = get_frames_per_file(

setup.py

@@ -22,7 +22,7 @@
 
 setuptools.setup(
     name="hdf5maker",
-    version= '2023.9.21.dev0',
+    version= '2024.2.9.dev0',
     author="Erik Frojdh",
     author_email="[email protected]",
     description="Eiger raw file to hdf5 converter",
@@ -36,5 +36,5 @@
         "Operating System :: OS Independent",
     ],
     ext_modules=[c_ext],
-    python_requires='>=3.8',
+    python_requires='>=3.9',
 )