update image writing api

README.md

@@ -15,10 +15,19 @@ python3 -m pip install -e .
 ```
 
 Running the self-test must be done on a Raspberry Pi with camera module:
-```python
+```sh
+python3 -m pip install -e .[tests]
+
 python3 -m pytest
 ```
 
+To install advanced (HDF5, NetCDF4) image writing libraries:
+```sh
+apt install libhdf5-dev
+
+python3 -m pip install -e .[io]
+```
+
 ### Tips
 * Avoid MMAL errors: `raspi-config` → Advanced Options → Memory Split should be 128 MB, not 64 MB.
 * Fix error "ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory" by:

getrawimage.py

@@ -22,7 +22,7 @@ def main():
     # NOTE: Didn't use SIGINT to allow camera to cleanup/close--avoid GPU memory leaks!
     p = ArgumentParser(description='Raspberry Pi Picamera demo with raw Bayer data')
     p.add_argument('exposure', help='exposure time [seconds]', type=float)
-    p.add_argument('outfn', help='HDF5 or TIFF file to write image stack to', nargs='?')
+    p.add_argument('outfn', help='HDF5, NetCDF4 or TIFF file to write image stack to', nargs='?')
     p.add_argument('-n', '--numimg', help='number of images to write to disk', type=int, default=10)
     p.add_argument('-8', '--bit8', help="convert output to 8-bit", action='store_true')
     p.add_argument('-p', '--plot', help='show via Matplotlib (slow)s', action='store_true')

pibayer/io.py

@@ -27,7 +27,7 @@ def writeframes(outfn: Path, img: xarray.DataArray):
         import h5py
         with h5py.File(outfn, 'w') as f:
             f.create_dataset(KEY,
-                             data=img,
+                             data=img.values,
                              shape=img.shape,
                              dtype=img.dtype,
                              compression='gzip',
@@ -37,6 +37,6 @@ def writeframes(outfn: Path, img: xarray.DataArray):
 
             for k, v in img.attrs.items():
                 f[k] = v
-    elif outfn.suffix in ('.tif', '.tiff'):  # TIFF
+    else:  # assume stacked image format
         import imageio
-        imageio.imsave(outfn, img)
+        imageio.mimwrite(outfn, img.values)

setup.cfg

@@ -35,6 +35,7 @@ install_requires =
   picamera
   numpy
   xarray
+  imageio>=2.3
 
 [options.extras_require]
 tests =