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jimrybarski / nd2reader

Pure Python library for reading NIS Elements ND2 images and metadata
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This ND2 has no recorded start time #100

Closed simone-codeluppi closed 8 years ago

simone-codeluppi commented 8 years ago

Hi I tried to run nd2reader to convert a multiposition (xyz) file with two channels and I get a no recorded time error (I guess it is missing in the DB). I pasted the traceback below.

Thanks a lot! this tool will really help me!

Simone

ValueError Traceback (most recent call last)

in () ----> 1 nd2file=nd2.Nd2('/Users/simone/Desktop/test/ND2conversion/Other_ND2/Testformat.nd2') /Users/simone/Desktop/smFISH-analysis-package/nd2reader-master/nd2reader/interface.py in **init**(self, filename) 17 major_version, minor_version = get_version(self._fh) 18 parser = get_parser(self._fh, major_version, minor_version) ---> 19 self._driver = parser.driver 20 self._metadata = parser.metadata 21 /Users/simone/Desktop/smFISH-analysis-package/nd2reader-master/nd2reader/parser/v3.py in driver(self) 31 @property 32 def driver(self): ---> 33 return V3Driver(self.metadata, self._label_map, self._fh) 34 35 def _parse_metadata(self): /Users/simone/Desktop/smFISH-analysis-package/nd2reader-master/nd2reader/parser/v3.py in metadata(self) 26 def metadata(self): 27 if not self._metadata: ---> 28 self._parse_metadata() 29 return self._metadata 30 /Users/simone/Desktop/smFISH-analysis-package/nd2reader-master/nd2reader/parser/v3.py in _parse_metadata(self) 49 width = metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiWidth')] 50 channels = self._parse_channels(metadata_dict) ---> 51 date = self._parse_date(metadata_dict) 52 fields_of_view = self._parse_fields_of_view(metadata_dict) 53 frames = self._parse_frames(metadata_dict) /Users/simone/Desktop/smFISH-analysis-package/nd2reader-master/nd2reader/parser/v3.py in _parse_date(self, metadata_dict) 79 continue 80 return absolute_start_12 if absolute_start_12 else absolute_start_24 ---> 81 raise ValueError("This ND2 has no recorded start time. This is probably a bug.") 82 83 def _parse_channels(self, metadata_dict): ValueError: This ND2 has no recorded start time. This is probably a bug.
jimrybarski commented 8 years ago

I believe I've fixed this. Could you install branch 101-dont-require-date and see if it works?

jimrybarski commented 8 years ago

Alternatively @simone-codeluppi if you want to send me a copy (or partial copy) of your Nd2 I'd be happy to check myself.

simone-codeluppi commented 8 years ago

Hi! I managed to load the .nd2 file and get each image in numpy array. Thanks a lot to fix the issue! really appreciated! Simone