conflicting dimensions for 'ping_time' and 'ping_time': 'transmit_frequency_start' #1475
Description
General description of problem
My EK80 files do not convert to echopype objects, using echopype 0.9.0 or 0.10.0.
I use echopype's open_raw to try to convert to an echodata object, but it fails for all files.
Here is the related code statement and error (full code and output are provided in the next sections).
ed = ep.open_raw( rawfile , sonar_model='EK80' )
Error:
ValueError: conflicting sizes for dimension 'ping_time': length 113 on 'ping_time' and length 50 on {'ping_time': 'transmit_frequency_start'}
Echopype version
echopype v0.10.0
How did you install Echopype (e.g., conda or pip)
installed echopype using pip
What is your operating system
windows
Minimal code example
The following code reproduces the error:
``
imports
import echopype as ep
print( f"echopype version: {ep.version}" )
import os
Read raw EK80 data file to echopype object
Following example from https://echopype.readthedocs.io/en/stable/convert.html
inpath = r'example_data/test'
rawfn = r'WBAT-EK80-TEST-0907-T235739.raw'
rawfile = os.path.join( inpath, rawfn )
ed = ep.open_raw( rawfile , sonar_model='EK80' )
Error message printouts
Full output:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[4], line 12
8 rawfn = r'WBAT-EK80-TEST-0907-T235739.raw'
10 rawfile = os.path.join( inpath, rawfn )
---> 12 ed = ep.open_raw( rawfile , sonar_model='EK80' )
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\echopype\utils\prov.py:237, in add_processing_level.<locals>.wrapper.<locals>.inner(*args, **kwargs)
235 @functools.wraps(func)
236 def inner(*args, **kwargs):
--> 237 dataobj = func(*args, **kwargs)
238 if is_echodata:
239 ed = dataobj
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\echopype\convert\api.py:516, in open_raw(raw_file, sonar_model, xml_path, include_bot, include_idx, convert_params, storage_options, use_swap, max_chunk_size)
513 tree_dict["Sonar"] = None
515 # Set multi beam groups
--> 516 beam_groups = setgrouper.set_beam()
518 beam_group_type = []
519 for idx, beam_group in enumerate(beam_groups, start=1):
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\echopype\convert\set_groups_ek80.py:1202, in SetGroupsEK80.set_beam(self)
1200 for ch in self.sorted_channel["all"]:
1201 if ch in self.sorted_channel["complex"]:
-> 1202 ds_data = self._assemble_ds_complex(ch)
1203 elif ch in self.sorted_channel["power"]:
1204 ds_data = self._assemble_ds_power(ch)
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\echopype\convert\set_groups_ek80.py:891, in SetGroupsEK80._assemble_ds_complex(self, ch)
848 data_shape = self.parser_obj.ping_data_dict["complex"][ch]["real"].shape
849 ds_tmp = xr.Dataset(
850 {
851 "backscatter_r": (
(...) 888 },
889 )
--> 891 ds_tmp = self._add_freq_start_end_ds(ds_tmp, ch)
893 return set_time_encodings(ds_tmp)
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\echopype\convert\set_groups_ek80.py:817, in SetGroupsEK80._add_freq_start_end_ds(self, ds_tmp, ch)
813 return ds_tmp
815 print( f"L815*********************\nds_tmp \n{ds_tmp}\n*********************")
--> 817 ds_f_start_end = xr.Dataset(
818 {
819 "transmit_frequency_start": (
820 ["ping_time"],
821 freq_start.astype(float),
822 self._varattrs["beam_var_default"]["transmit_frequency_start"],
823 ),
824 "transmit_frequency_stop": (
825 ["ping_time"],
826 freq_stop.astype(float),
827 self._varattrs["beam_var_default"]["transmit_frequency_stop"],
828 ),
829 },
830 coords={
831 "ping_time": (
832 ["ping_time"],
833 self.parser_obj.ping_time[ch],
834 self._varattrs["beam_coord_default"]["ping_time"],
835 ),
836 },
837 )
839 ds_tmp = xr.merge(
840 [ds_tmp, ds_f_start_end], combine_attrs="override"
841 ) # override keeps the Dataset attributes
843 return ds_tmp
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\xarray\core\dataset.py:747, in Dataset.__init__(self, data_vars, coords, attrs)
744 if isinstance(coords, Dataset):
745 coords = coords._variables
--> 747 variables, coord_names, dims, indexes, _ = merge_data_and_coords(
748 data_vars, coords
749 )
751 self._attrs = dict(attrs) if attrs else None
752 self._close = None
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\xarray\core\dataset.py:460, in merge_data_and_coords(data_vars, coords)
456 coords = create_coords_with_default_indexes(coords, data_vars)
458 # exclude coords from alignment (all variables in a Coordinates object should
459 # already be aligned together) and use coordinates' indexes to align data_vars
--> 460 return merge_core(
461 [data_vars, coords],
462 compat="broadcast_equals",
463 join="outer",
464 explicit_coords=tuple(coords),
465 indexes=coords.xindexes,
466 priority_arg=1,
467 skip_align_args=[1],
468 )
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\xarray\core\merge.py:705, in merge_core(objects, compat, join, combine_attrs, priority_arg, explicit_coords, indexes, fill_value, skip_align_args)
700 prioritized = _get_priority_vars_and_indexes(aligned, priority_arg, compat=compat)
701 variables, out_indexes = merge_collected(
702 collected, prioritized, compat=compat, combine_attrs=combine_attrs
703 )
--> 705 dims = calculate_dimensions(variables)
707 coord_names, noncoord_names = determine_coords(coerced)
708 if compat == "minimal":
709 # coordinates may be dropped in merged results
File D:\ProgramData\Anaconda3\envs\echopype10\Lib\site-packages\xarray\core\variable.py:3022, in calculate_dimensions(variables)
3020 last_used[dim] = k
3021 elif dims[dim] != size:
-> 3022 raise ValueError(
3023 f"conflicting sizes for dimension {dim!r}: "
3024 f"length {size} on {k!r} and length {dims[dim]} on {last_used!r}"
3025 )
3026 return dims
ValueError: conflicting sizes for dimension 'ping_time': length 113 on 'ping_time' and length 50 on {'ping_time': 'transmit_frequency_start'}Example data
I can share a small file if someone can take a look at this problem.
Related existing issues or PRs
I have not seen similar issues reported.
Troubleshooting steps
No response