Merge branch 'edf' into 'master'

Support for output EDF format

Closes #211

See merge request !101

nabu/io/writer.py

@@ -11,6 +11,10 @@ from ..misc.utils import rescale_data
 from .config import export_dict_to_h5
 from .utils import check_h5py_version # won't be necessary once h5py >= 3.0 required
 
+try:
+    from silx.third_party.EdfFile import EdfFile
+except ImportError:
+    EdfFile = None
 try:
     from glymur import Jp2k
     __have_jp2k__ = True
@@ -282,6 +286,57 @@ class TIFFWriter(Writer):
             return path.dirname(self.fname)
 
 
+class EDFWriter(Writer):
+    def __init__(self, fname, start_index=0, filemode="w"):
+        """
+        EDF (ESRF Data Format) writer.
+
+        Parameters
+        -----------
+        fname: str
+            Path to the output file name
+        start_index: int, optional
+            When writing a stack of images, each image is written in a dedicated file
+            In this case, the output is a series of files `filename_0000.tif`,
+            `filename_0001.edf`, etc. This parameter is the starting index for
+            file names.
+        """
+        super().__init__(fname)
+        self.filemode = filemode
+        self.start_index = start_index
+
+    def _write_edf(self, data, config=None, filename=None, filemode=None):
+        if filename is None:
+            filename = self.fname
+        edf = EdfFile(filename)
+        config = config or {}
+        config["software"] = str("nabu %s" % version)
+        config["date"] = get_datetime()
+        edf.WriteImage(
+            config,
+            data
+        )
+        edf = None
+
+
+    def write(self, data, *args, config=None, **kwargs):
+        if data.ndim < 3:
+            self._write_edf(data, config=config)
+            return
+        if (data.ndim == 3) and (data.shape[0] == 1):
+            self._write_edf(data[0], config=config)
+            return
+        dirname, rel_filename = path.split(self.fname)
+        prefix, ext = path.splitext(rel_filename)
+        for i in range(data.shape[0]):
+            curr_rel_filename = prefix + str("_%04d" % (self.start_index + i)) + ext
+            fname = path.join(dirname, curr_rel_filename)
+            self._write_edf(data[i], filename=fname, config=config)
+
+    def get_filename(self):
+        return path.dirname(self.fname)
+
+
 class JP2Writer(Writer):
     def __init__(self, fname, start_index=0, filemode="wb", psnr=None, auto_convert=True):
         """
@@ -379,5 +434,6 @@ Writers = {
     "j2k": JP2Writer,
     "jp2": JP2Writer,
     "jp2k": JP2Writer,
+    "edf": EDFWriter,
 }
 

nabu/resources/nabu_config.py

@@ -309,7 +309,7 @@ nabu_config = {
         },
         "file_format": {
             "default": "hdf5",
-            "help": "Output file format. Available are: hdf5, tiff, jp2",
+            "help": "Output file format. Available are: hdf5, tiff, jp2, edf",
             "validator": output_file_format_validator,
             "type": "optional",
         },

nabu/resources/params.py

@@ -92,6 +92,7 @@ files_formats = {
     "jp2k": "jp2",
     "j2k": "jp2",
     "jpeg2000": "jp2",
+    "edf": "edf",
 }
 class FileFormat(Enum):
     EDF = "edf"