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Reduce code complexity

zolfa-add_slices_loading
Ruben Verweij 8 years ago
parent
commit
6f151e8701
1 changed files with 33 additions and 24 deletions
  1. +33
    -24
      nd2reader/parser/v3.py

+ 33
- 24
nd2reader/parser/v3.py View File

@ -181,23 +181,32 @@ class V3Parser(BaseParser):
""" """
for line in raw_metadata.image_text_info[six.b('SLxImageTextInfo')].values(): for line in raw_metadata.image_text_info[six.b('SLxImageTextInfo')].values():
line = line.decode("utf8") line = line.decode("utf8")
absolute_start_12 = None
absolute_start_24 = None
# ND2s seem to randomly switch between 12- and 24-hour representations. # ND2s seem to randomly switch between 12- and 24-hour representations.
try:
absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S")
except (TypeError, ValueError):
pass
try:
absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p")
except (TypeError, ValueError):
pass
absolute_start_24 = self._parse_date_24h(line)
absolute_start_12 = self._parse_date_12h(line)
if not absolute_start_12 and not absolute_start_24: if not absolute_start_12 and not absolute_start_24:
continue continue
return absolute_start_12 if absolute_start_12 else absolute_start_24 return absolute_start_12 if absolute_start_12 else absolute_start_24
return None return None
def _parse_channels(self, raw_metadata):
@staticmethod
def _parse_date_12h(line):
try:
absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p")
return absolute_start_12
except (TypeError, ValueError):
return None
@staticmethod
def _parse_date_24h(line):
try:
absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S")
return absolute_start_24
except (TypeError, ValueError):
return None
@staticmethod
def _parse_channels(raw_metadata):
""" """
These are labels created by the NIS Elements user. Typically they may a short description of the filter cube These are labels created by the NIS Elements user. Typically they may a short description of the filter cube
used (e.g. "bright field", "GFP", etc.) used (e.g. "bright field", "GFP", etc.)
@ -256,7 +265,8 @@ class V3Parser(BaseParser):
""" """
return self._parse_dimension(r""".*?Z\((\d+)\).*?""", raw_metadata) return self._parse_dimension(r""".*?Z\((\d+)\).*?""", raw_metadata)
def _parse_dimension_text(self, raw_metadata):
@staticmethod
def _parse_dimension_text(raw_metadata):
""" """
While there are metadata values that represent a lot of what we want to capture, they seem to be unreliable. While there are metadata values that represent a lot of what we want to capture, they seem to be unreliable.
Sometimes certain elements don't exist, or change their data type randomly. However, the human-readable text Sometimes certain elements don't exist, or change their data type randomly. However, the human-readable text
@ -266,18 +276,16 @@ class V3Parser(BaseParser):
:rtype: str :rtype: str
""" """
for line in raw_metadata.image_text_info[six.b('SLxImageTextInfo')].values():
dimension_text = six.b("")
textinfo = raw_metadata.image_text_info[six.b('SLxImageTextInfo')].values()
for line in textinfo:
if six.b("Dimensions:") in line: if six.b("Dimensions:") in line:
metadata = line
break
else:
return six.b("")
for line in metadata.split(six.b("\r\n")):
if line.startswith(six.b("Dimensions:")):
dimension_text = line
break
else:
return six.b("")
entries = line.split(six.b("\r\n"))
for entry in entries:
if entry.startswith(six.b("Dimensions:")):
return entry
return dimension_text return dimension_text
def _parse_dimension(self, pattern, raw_metadata): def _parse_dimension(self, pattern, raw_metadata):
@ -298,7 +306,8 @@ class V3Parser(BaseParser):
count = int(match.group(1)) count = int(match.group(1))
return list(range(count)) return list(range(count))
def _parse_total_images_per_channel(self, raw_metadata):
@staticmethod
def _parse_total_images_per_channel(raw_metadata):
""" """
The total number of images per channel. Warning: this may be inaccurate as it includes "gap" images. The total number of images per channel. Warning: this may be inaccurate as it includes "gap" images.


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