Merge pull request #2 from starcalibre/dib-support

Add support for DIB files and large data sets

README.md

@@ -1,7 +1,7 @@
 cellom2tif
 ==========
 
-Python script to convert Cellomics .C01 files to TIFF.
+Python script to convert Cellomics files to TIFF.
 
 Read the BioFormats [report card for Cellomics
 files](https://www.openmicroscopy.org/site/support/bio-formats5/formats/cellomics.html).
@@ -37,17 +37,18 @@ GPL* by the import of Python BioFormats.  Consult your lawyer.
 $ cellom2tif -h
 usage: cellom2tif [-h] [-E FILENAME] [-m] [-v] root_path out_path
 
-Convert a bunch of Cellomics .C01 files to TIFFs.
+Convert a bunch of Cellomics files to TIFFs. Currently supports the .CO1 and 
+.DIB format.
 
 positional arguments:
-  root_path             The path containing .C01 files
+  root_path             The path containing the Cellomics files
   out_path              The path to output the TIFFs.
 
 optional arguments:
   -h, --help            show this help message and exit
   -E FILENAME, --error-file FILENAME
                         Log problem filenames to the given filename.
-  -m, --ignore-masks    Ignore files ending in "o1.C01".
+  -m, --ignore-masks    Ignore files ending in "o1".
   -v, --verbose         Print out runtime information.
 ```
 

cellom2tif/cellom2tif.py

@@ -72,6 +72,7 @@ def read_image(filelike):
     else:
         rdr = bf.ImageReader(filelike)
     image = rdr.read(rescale=False)
+    rdr.close()
     return image
 
 

cellom2tif/filetypes.py

@@ -1,3 +1,33 @@
+import os
+
+
+def has_extension(filename, ext):
+    """
+    Determine whether a file has a particular extension.
+
+    Parameters
+    ----------
+    filename : string
+        The filename of the query file.
+    ext : string
+        The extension being checked.
+
+    Returns
+    -------
+    file_has_ext : bool
+        True if the filename has the specified extension.
+
+    Examples
+    --------
+    >>> dib_file = 'AS_09125_050116110001_A01f00d0.DIB'
+    >>> has_extension(dib_file, 'dib')
+    True
+    """
+    fn_ext = os.path.splitext(filename)[1][1:]
+    file_has_ext = fn_ext.lower() == ext.lower()
+    return file_has_ext
+
+
 def is_cellomics_image(fn):
     """Determine whether a file is a Cellomics image.
 
@@ -11,7 +41,7 @@ def is_cellomics_image(fn):
     is_cellom : bool
         True if the filename points to a Cellomics image.
     """
-    is_cellom = fn.endswith('.C01') or fn.endswith('.c01')
+    is_cellom = has_extension(fn, 'C01') or has_extension(fn, 'DIB')
     return is_cellom
 
 
@@ -27,8 +57,13 @@ def is_cellomics_mask(fn):
     -------
     is_mask : bool
         True if the filename points to a Cellomics mask image.
+
+    Examples
+    --------
+    >>> mask_fn = 'MFGTMP_120628160001_C18f00o1.C01'
+    >>> is_cellomics_mask(mask_fn)
+    True
     """
-    is_mask = fn.endswith('o1.C01') or fn.endswith('o1.c01')
+    base_fn = os.path.splitext(fn)[0]
+    is_mask = base_fn.endswith('o1') or base_fn.endswith('o1')
     return is_mask
-
-