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Looking for IDL Structures to Python compatible HDF5 Examples [message #91813]

Tue, 01 September 2015 10:33

eben.pendleton
Messages: 2
Registered: September 2015

Junior Member

Hi all,

I'm looking for code examples of writing ODL structures to HDF5 tables that can be read in Python (2.7). Filenames are removed

I've tried the following approach using the IDL coyote guide to create the file in IDL 7.1:

pro write_idl_struct_to_hdf5,struct,dir_out,outfile

file = dir_out+outfile+'.h5'
fid = H5F_CREATE(file)

datatype_id = H5T_IDL_CREATE(struct)
dataspace_id=H5S_CREATE_SIMPLE(1) ; not so simple..

dataset_id = H5D_CREATE(fid,'o',datatype_id,dataspace_id)
H5D_WRITE, dataset_id, struct

H5S_CLOSE, dataspace_id
H5T_CLOSE, datatype_id

H5F_CLOSE, fid

print,'---Finished Writing IDL struct to HDF5---'
end

Python code and Error
import pandas as pd
dir_in=r'C:\D_Drive\Python\hdf5'
infile=...

mynewdf = pd.HDFStore(dir_in+'\\'+infile)
print(mynewdf)

print(mynewdf.select('o',columns='TASK_NAME'))

resulting in:
<class 'pandas.io.pytables.HDFStore'>
File path: ...
/o frame_table [0.0.0] (typ->generic,nrows->1,ncols->63,indexers->[index],dc-> [TASK_CODE,TASK_NAME,EVENT,SYS_LOC_CODE,SUBFACILITY_CODE,ARE A,RIVER_STREAM_MILE,MILES_FROM_NC_MOUTH,X_COORD,Y_COORD,COOR D_TYPE_CODE,REFERENCE_POINT,ELEV,ELEV_UNIT,ELEV_COLLECT_METH OD_CODE,ELEV_DATUM_CODE,WATER_COLUMN_DEPTH,WATER_COLUMN_DEPT H_UNIT_CODE,SYS_SAMPLE_CODE,PARENT_SAMPLE_CODE,MATRIX_CODE,L AB_MATRIX_CODE,SAMPLE_TYPE_CODE,SAMPLE_DATE,START_DEPTH,END_ DEPTH,DEPTH_UNIT,DEPTH_INTERVAL,SEDIMENT_NATIVE,GROUP_DESC,C HEMICAL_NAME,CAS_RN,FRACTION,ANALYTIC_METHOD,LEACHATE_METHOD ,PREP_METHOD,RESULT_VALUE,LAB_QUALIFIERS,VALIDATOR_QUALIFIER S,INTERPRETED_QUALIFIERS,DETECT_FLAG,TARGET_UNIT,REPORTABLE_ RESULT,VALIDATED_YN,VALIDATOR_REASON_CODE,BASIS,METHOD_DETEC TION_LIMIT,REPORTING_DETECTION_LIMIT,DILUTION_FACTOR,LAB_NAM E_CODE,LAB_SAMPLE_ID,ANL_SHORT_NAME,PARENT_LOC_CODE,DATA_REL EASE_STATUS,DATA_ANALYSIS_HIERARCHY,RESULT_VALUE_MDL,RISK_SC REEN_USABILITY,BASELINE_RA_USABILITY,CAS_RN_4PROUCL,CHEMICAL _NAME_4PROUCL,TREATMENT_FLAG_4PROUCL,CHEMICAL_NAME_4LABEL,US ABILITY_HIERARCHY])

The error generated is
ValueError: Wrong number of items passed 283774, placement implies 1

The 283774 number is the number of rows in the structure and it seems that each tag in the dataframe has one row with 283774 elements.

Is there some layout adjustment that's needed to read a structure correctly in HDF5?

Eben

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[Message index]

		Looking for IDL Structures to Python compatible HDF5 Examples By: eben.pendleton on Tue, 01 September 2015 10:33
		Re: Looking for IDL Structures to Python compatible HDF5 Examples By: markb77 on Tue, 01 September 2015 10:49
		Re: Looking for IDL Structures to Python compatible HDF5 Examples By: Alain Kattnig on Wed, 02 September 2015 00:20
		Re: Looking for IDL Structures to Python compatible HDF5 Examples By: eben.pendleton on Wed, 09 September 2015 13:28
		Re: Looking for IDL Structures to Python compatible HDF5 Examples By: markb77 on Thu, 10 September 2015 14:04
		Re: Looking for IDL Structures to Python compatible HDF5 Examples By: marcomottola87 on Wed, 17 May 2017 03:41

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