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resolves #1 hopefully

zolfa-add_slices_loading
jim 10 years ago
parent
commit
5ef69bca41
1 changed files with 54 additions and 9 deletions
  1. +54
    -9
      nd2reader/service/__init__.py

+ 54
- 9
nd2reader/service/__init__.py View File

@ -1,6 +1,9 @@
# -*- coding: utf-8 -*-
import array
import numpy as np
import struct
import re
from StringIO import StringIO
from collections import namedtuple
import logging
@ -69,12 +72,11 @@ class BaseNd2(object):
:rtype: int
"""
return self._image_count / self.field_of_view_count / self.z_level_count
return self._reader.time_index_count
@property
def z_level_count(self):
# return self._image_count / self._sequence_count
return 3
return self._reader.z_level_count
@property
def field_of_view_count(self):
@ -85,11 +87,7 @@ class BaseNd2(object):
NIS Elements can figure it out, but we haven't found it yet.
"""
try:
valid_fovs = self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['pItemValid']
except KeyError:
valid_fovs = self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['pItemValid']
return sum(valid_fovs)
return self._reader.field_of_view_count
@property
def channel_count(self):
@ -124,6 +122,23 @@ class Nd2Reader(object):
self._metadata = {}
self._read_map()
self._parse_dict_data()
self.__dimensions = None
@property
def _dimensions(self):
if self.__dimensions is None:
# TODO: Replace this with a single regex
for line in self._metadata['ImageTextInfo']['SLxImageTextInfo'].values():
if "Dimensions:" in line:
metadata = line
break
else:
raise Exception("Could not parse metadata dimensions!")
for line in metadata.split("\r\n"):
if line.startswith("Dimensions:"):
self.__dimensions = line
break
return self.__dimensions
@property
def fh(self):
@ -131,9 +146,39 @@ class Nd2Reader(object):
self._file_handler = open(self._filename, "rb")
return self._file_handler
@property
def time_index_count(self):
"""
The number of images for a given field of view, channel, and z_level combination.
Effectively the number of frames.
:rtype: int
"""
pattern = r""".*?T'\((\d+)\).*?"""
return int(re.match(pattern, self._dimensions).group(1))
@property
def z_level_count(self):
pattern = r""".*?Z\((\d+)\).*?"""
return int(re.match(pattern, self._dimensions).group(1))
@property
def field_of_view_count(self):
"""
The metadata contains information about fields of view, but it contains it even if some fields
of view were cropped. We can't find anything that states which fields of view are actually
in the image data, so we have to calculate it. There probably is something somewhere, since
NIS Elements can figure it out, but we haven't found it yet.
"""
pattern = r""".*?XY\((\d+)\).*?"""
return int(re.match(pattern, self._dimensions).group(1))
@property
def channel_count(self):
return self._metadata['ImageAttributes']["SLxImageAttributes"]["uiComp"]
pattern = r""".*?λ\((\d+)\).*?"""
return int(re.match(pattern, self._dimensions).group(1))
def get_raw_image_data(self, image_set_number, channel_offset):
chunk = self._label_map["ImageDataSeq|%d!" % image_set_number]


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