Merge pull request #554 from psavery/edf-ge-format

LGTM. Thanks for the contribution

src/fabio/GEimage.py

@@ -41,8 +41,12 @@
 import io
 import numpy
 import struct
+from .edfimage import EdfImage
 from .fabioimage import FabioImage
 from .fabioutils import next_filename, previous_filename
+from .openimage import MAGIC_NUMBERS
+
+EDF_MAGIC_NUMBERS = [(x, y) for x, y in MAGIC_NUMBERS if y == 'edf']
 
 GE_HEADER_INFO = [
     # Name, length in bytes, format for struct (None means string)
@@ -265,6 +269,20 @@ def _readheader(self, infile):
                     raise IOError("GE file size is incorrect")
                 nframes = file_size // bytes_per_frames
                 self.header['NumberOfFrames'] = nframes
+        elif any(self.header["ImageFormat"].startswith(x) for x, _ in EDF_MAGIC_NUMBERS):
+            # At APS, they started saving some GE headers with an EDF format in ~2022
+
+            # Use the same metadata as the blank header...
+            self.header.update(self.BLANKED_HEADER_METADATA)
+
+            # Read the EDF header
+            cur = infile.tell()
+            infile.seek(0)
+            header = EdfImage._read_header_block(infile, 1)
+            infile.seek(cur, io.SEEK_SET)
+
+            # Extract any needed info from the EDF header
+            self.header['NumberOfFrames'] = int(header[0]["Num_Images"])
 
     def read(self, fname, frame=None):
         """Read header into self.header and the data into self.data."""

src/fabio/openimage.py

@@ -42,7 +42,9 @@
 
 import os.path
 import logging
+import re
 from . import fabioutils
+from .compression import ExternalCompressors
 from .fabioutils import FilenameObject, BytesIO
 from .fabioimage import FabioImage
 
@@ -149,6 +151,18 @@ def do_magic(byts, filename):
                         return "marccd"
                     else:
                         return "tif"
+
+            if format_type == "edf" and isinstance(filename, str):
+                # Might be GE with an EDF header. Check the extension.
+                extension = filename.split(".")[-1]
+                # If it is a compression extension, check the next one up.
+                if f'.{extension}' in ExternalCompressors.COMMANDS:
+                    extension = filename.split(".")[-2]
+
+                # If the extension is `ge` plus a number, assume it is GE
+                if re.search(r'^ge\d*$', extension):
+                    return "GE"
+
             return format_type
     raise Exception("Could not interpret magic string")
 

src/fabio/test/codecs/test_geimage.py

@@ -53,6 +53,7 @@ class TestGE(unittest.TestCase):
         ("GE_aSI_detector_image_1529", (2048, 2048), (1515, 16353, 1833.0311, 56.9124)),
         ("GE_image_1frame_intact_header.ge", (2048, 2048), (1515, 16353, 2209.1113, 437.6377)),
         ("GE_image_1frame_blanked_header.ge", (2048, 2048), (1300, 16349, 1886.41111, 117.0603)),
+        ("dark_before_000428.edf.ge5", (2048, 2048), (1300, 16349, 1833.87892, 84.5265)),
     ]
 
     def setUp(self):