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Write IGOR binary (.ibw) or text (.itx) files from numpy array

Project description

IgorWriter

Write IGOR binary (.ibw) or text (.itx) files from numpy array

Installation

$ pip install igorwriter

Usage

>>> import numpy as np
>>> from igorwriter import IgorWave
>>> array = np.array([1,2,3,4,5,6])
>>> wave = IgorWave(array, name='mywave')
>>> wave2 = IgorWave(array.astype(np.float32), name='mywave2')
>>> wave.set_datascale('DataUnit')
>>> wave.set_dimscale('x', 0, 0.01, 's')  # set x scale information
>>> wave.save('mywave.ibw')  # Igor Binary Wave files can only contain one wave per file
>>> wave.save_itx('mywave.itx')
>>> with open('multi_waves.itx', 'w') as fp:  # Igor Text files can contain multiples waves per file
>>>     wave.save_itx(fp)
>>>     wave2.save_itx(fp)

Wave Names

There are restrictions on object names in IGOR. From v0.2.0, this package deals with illegal object names.

>>> wave = IgorWave(array, name='\'this_is_illegal\'', on_errors='fix')  # fix illegal names automatically
RenameWarning: name "'this_is_illegal'" is fixed as '_this_is_illegal_' (reason: name must not contain " ' : ; or any control characters.)
>>> print(wave.name)
_this_is_illegal_
>>> wave = IgorWave(array, name='\'this_is_illegal\'', on_errors='raise')  # raise errors
Traceback (most recent call last):
...
igorwriter.validator.InvalidNameError: name must not contain " ' : ; or any control characters.

Exporting pandas.DataFrame

Convenience functions for saving DataFrame in a Igor Text file or a series of Igor Binary Wave files are provided.

>>> from igorwriter import utils
>>> utils.dataframe_to_itx(df, 'df.itx')   # all Series are exported in one file
>>> waves = utils.dataframe_to_ibw(df, prefix='df_bin')   # each Series is saved in a separate file, <prefix>_<column>.ibw
>>> waves  # dictionary of generated IgorWaves. You can change wave names, set data units, set dimension scaling, etc.
{'col1': <IgorWave 'col1' at 0x...>, 'col2': ...}

Notes on Image Plots

Image Plot in IGOR and imshow in matplotlib use different convention for x and y axes:

  • Rows as x, columns as y (IGOR)
  • Columns as x, rows as y (Matplotlib)

Thus, image parameter was introduced in save() and save_itx() methods. If you use e.g.

>>> wave.save('path.ibw', image=True)

plt.imshow and Image Plot will give the same results.

Changelog

v0.3.0 (2019-11-16)

  • Added utils.dict_to_{ibw, itx}
  • Set datascale automatically for pint Quantity object.
  • Added support for np.datetime64 array.

v0.2.3 (2019-11-09)

  • Added support for 64-bit integers (by automatically casting onto 32-bit integers on save).

v0.2.0 (2019-11-08)

  • Added utilities for pandas (utils.dataframe_to_{ibw, itx} ).
  • Added unittest scripts.
  • Added wave name validator.
  • BUG FIX: long (> 3 bytes) units for dimension scaling were ignored in save_itx()
  • IgorWriter now uses system locale encoding rather than ASCII (the default behavior of IGOR Pro prior to ver. 7.00)

Project details


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