Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improve image reader selection function #157

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Improve image reader selection function #157

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
5b950ed
Add allow_open_files parameter
DavidStirling Feb 23, 2022
4c606bf
Implement per-plane indexing with czt
DavidStirling Mar 17, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
75 changes: 26 additions & 49 deletions bioformats/formatreader.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -556,8 +556,7 @@ class ImageReader(object):
that can be used to cache the file contents in memory.

'''

def __init__(self, path=None, url=None, perform_init=True):
def __init__(self, path=None, url=None, perform_init=True, allow_open_files=True):
self.stream = None
file_scheme = "file:"
self.using_temp_file = False
Expand Down Expand Up @@ -621,54 +620,20 @@ def __init__(self, path=None, url=None, perform_init=True):
"The file, \"%s\", does not exist." % path,
path)

self.stream = jutil.make_instance('loci/common/RandomAccessInputStream',
'(Ljava/lang/String;)V',
self.path)

self.rdr = None
class_list = get_class_list()
IFormatReader = make_iformat_reader_class()
self.rdr = IFormatReader()
find_rdr_script = """
var classes = class_list.getClasses();
var rdr = null;
var lc_filename = java.lang.String(filename.toLowerCase());
for (pass=0; pass < 3; pass++) {
for (class_idx in classes) {
var maybe_rdr = classes[class_idx].newInstance();
if (pass == 0) {
if (maybe_rdr.isThisType(filename, false)) {
rdr = maybe_rdr;
break;
}
continue;
} else if (pass == 1) {
var suffixes = maybe_rdr.getSuffixes();
var suffix_found = false;
for (suffix_idx in suffixes) {
var suffix = java.lang.String(suffixes[suffix_idx]);
suffix = suffix.toLowerCase();
if (lc_filename.endsWith(suffix)) {
suffix_found = true;
break;
}
}
if (! suffix_found) continue;
}
if (maybe_rdr.isThisType(stream)) {
rdr = maybe_rdr;
break;
}
}
if (rdr) break;
}
importClass(Packages.loci.formats.ImageReader);
var reader = new ImageReader();
reader.setAllowOpenFiles(allow_open_files);
var rdr = reader.getReader(filename);
rdr;
"""
IFormatReader = make_iformat_reader_class()
jrdr = jutil.run_script(find_rdr_script, dict(class_list = class_list,
filename = filename,
stream = self.stream))
jrdr = jutil.run_script(find_rdr_script, dict(filename=self.path.lower(),
allow_open_files=allow_open_files))
if jrdr is None:
raise ValueError("Could not find a Bio-Formats reader for %s", self.path)
self.rdr = IFormatReader()
self.rdr.o = jrdr
if perform_init:
self.init_reader()
Expand Down Expand Up @@ -834,7 +799,9 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
index = self.rdr.getIndex(z,0,t)
image = np.frombuffer(openBytes_func(index), dtype)
image.shape = (height, width, self.rdr.getSizeC())
if image.shape[2] > 3:
if c is not None and len(image.shape) > 2:
image = image[:, :, c]
elif image.shape[2] > 3:
image = image[:, :, :3]
elif c is not None and self.rdr.getRGBChannelCount() == 1:
index = self.rdr.getIndex(z,c,t)
Expand Down Expand Up @@ -865,10 +832,12 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
for i in range(self.rdr.getSizeC())]
image = np.dstack(images)
image.shape = (height, width, self.rdr.getSizeC())
if not channel_names is None:
if channel_names is not None:
metadata = metadatatools.MetadataRetrieve(self.metadata)
for i in range(self.rdr.getSizeC()):
index = self.rdr.getIndex(z, 0, t)
# Indexing to get channel names can be unreliable.
# Assume all images in the series have the same names?
index = self.rdr.getIndex(0, 0, 0)
channel_name = metadata.getChannelName(index, i)
if channel_name is None:
channel_name = metadata.getChannelID(index, i)
Expand Down Expand Up @@ -929,13 +898,21 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
# The image reader cache associates path/url with a reader
__image_reader_cache = {}

def get_image_reader(key, path=None, url=None):

def get_image_reader(key, path=None, url=None, allow_open_files=True):
'''Make or find an image reader appropriate for the given path

path - pathname to the reader on disk.

key - use this key to keep only a single cache member associated with
that key open at a time.

allow_open_files - boolean. If True, bioformats is allowed to open file headers
to determine which reader to use. If False, only the file
extension can be used to pick a reader. Note that opening
files is absolutely required to properly detect some formats,
most notably OME-TIF. When only using extensions data can
be incorrect if the wrong reader is selected.
'''
logger.debug("Getting image reader for: %s, %s, %s" % (key, path, url))
if key in __image_reader_key_cache:
Expand All @@ -958,7 +935,7 @@ def get_image_reader(key, path=None, url=None):
rdr = OmeroReader(__omero_server, __omero_session_id, url=url)
else:
logger.debug("Falling back to Java reader.")
rdr = ImageReader(path=path, url=url)
rdr = ImageReader(path=path, url=url, allow_open_files=allow_open_files)
old_count = 0
__image_reader_cache[path, url] = (old_count+1, rdr)
__image_reader_key_cache[key] = (path, url)
Expand Down