https://github.com/waikato-datamining/spectral-data-converter
Python library for converting (and filtering) spectral data in various formats.
https://github.com/waikato-datamining/spectral-data-converter
conversion python3 spectral-data
Last synced: 5 months ago
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Python library for converting (and filtering) spectral data in various formats.
- Host: GitHub
- URL: https://github.com/waikato-datamining/spectral-data-converter
- Owner: waikato-datamining
- License: mit
- Created: 2025-06-11T04:16:45.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-08-04T03:06:09.000Z (11 months ago)
- Last Synced: 2025-08-04T05:58:08.832Z (11 months ago)
- Topics: conversion, python3, spectral-data
- Language: Python
- Homepage: https://www.data-mining.co.nz/spectral-data-converter-examples/
- Size: 266 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.rst
- License: LICENSE
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README
# spectral-data-converter
Python library for converting (and filtering) spectral data in various formats.
Some of the formats make use of the [wai_spectralio](https://github.com/waikato-datamining/wai-spectralio)
library and some of the filters use the [wai_ma](https://github.com/waikato-datamining/py-matrix-algorithms)
library for processing the data.
## Installation
Via PyPI:
```bash
pip install spectral_data_converter
```
The latest code straight from the repository:
```bash
pip install git+https://github.com/waikato-datamining/spectral-data-converter.git
```
## Docker
Docker images are available as well. Please see the following page por more information:
https://github.com/waikato-datamining/spectral-data-converter-all/tree/main/docker
## Dataset formats
The following dataset formats are supported:
| Format | Read | Write |
|:-------------------------------|:------------------------------|:---------------------------|
| [ADAMS](formats/adams.md) | [Y](plugins/from-adams.md) | [Y](plugins/to-adams.md) |
| [ARFF](formats/arff.md) | [Y](plugins/from-arff.md) | [Y](plugins/to-arff.md) |
| [ASC](formats/asc.md) | [Y](plugins/from-asc.md) | [Y](plugins/to-asc.md) |
| [ASCII XY](formats/asciixy.md) | [Y](plugins/from-asciixy.md) | [Y](plugins/to-asciixy.md) |
| CAL (FOSS) | [Y](plugins/from-cal.md) | [Y](plugins/to-cal.md) |
| CSV | [Y](plugins/from-csv.md) | [Y](plugins/to-csv.md) |
| [DPT](formats/dpt.md) | [Y](plugins/from-dpt.md) | [Y](plugins/to-dpt.md) |
| MPS | [Y](plugins/from-mps.md) | N |
| NIR (FOSS) | [Y](plugins/from-nir.md) | [Y](plugins/to-nir.md) |
| OPUS (Bruker) | [Y](plugins/from-opus.md) | N |
| OPUS Ext (Bruker) | [Y](plugins/from-opus-ext.md) | N |
| SPA (Thermo Scientific) | [Y](plugins/from-spa.md) | N |
The following sample data formats are supported:
| Format | Read | Write |
|:----------------------------------------|:-------------------------------|:-----------------------------|
| [ADAMS Report](formats/adams_report.md) | [Y](plugins/from-report-sd.md) | [Y](plugins/to-report-sd.md) |
| CSV | [Y](plugins/from-csv-sd.md) | [Y](plugins/to-csv-sd.md) |
| JSON | [Y](plugins/from-json-sd.md) | [Y](plugins/to-json-sd.md) |
## Tools
### Dataset conversion
```
usage: sdc-convert [-h] [--help-all] [--help-plugin NAME] [-u INTERVAL]
[-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-b]
[--placeholders FILE] [--load_pipeline FILE]
[--dump_pipeline FILE]
Tool for converting between spectral data formats.
readers (25):
from-adams, from-arff, from-asc, from-asciixy, from-cal, from-csv,
from-csv-sd, from-dpt, from-json-sd, from-mps, from-multi, from-nir,
from-opus, from-opus-ext, from-pyfunc, from-report-sd, from-spa,
from-storage, from-text-file, from-zip, get-email, list-files,
poll-dir, start, watch-dir
filters (41):
add-sampledata, apply-cleaner, attach-metadata, block, center,
check-duplicate-filenames, copy-files, delete-storage,
discard-by-name, downsample, equi-distance, list-to-sequence, log,
max-records, metadata, metadata-from-name, metadata-to-placeholder,
move-files, passthrough, pca, pls1, pyfunc-filter, randomize-records,
record-window, rename, row-norm, sample, savitzky-golay,
savitzky-golay2, set-metadata, set-placeholder, set-storage, simpls,
spectrum-to-sampledata, split-records, standard-normal-variate*,
standardize, stop, sub-process, tee, trigger
writers (20):
console, delete-files, send-email, to-adams, to-arff, to-asc,
to-asciixy, to-cal, to-csv, to-csv-sd, to-dpt, to-json-sd,
to-metadata, to-multi, to-nir, to-pyfunc, to-report-sd, to-storage,
to-text-file, to-zip
options:
-h, --help Show basic help message and exit.
--help-all Show basic help message plus help on all plugins and exit.
--help-plugin NAME Show help message for plugin NAME and exit.
-u, --update_interval INTERVAL
Outputs the progress every INTERVAL records (default: 1000).
-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
The logging level to use (default: WARN).
-b, --force_batch Processes the data in batches.
--placeholders FILE The file with custom placeholders to load (format: key=value).
--load_pipeline FILE The file to load the pipeline command from.
--dump_pipeline FILE The file to dump the pipeline command in.
```
### Executing pipeline multiple times
```
usage: sdc-exec [-h] --exec_generator GENERATOR [--exec_dry_run]
[--exec_prefix PREFIX] [--exec_placeholders FILE]
[--exec_format {cmdline,file}]
[--exec_logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
...
Tool for executing a pipeline multiple times, each time with a different set
of variables expanded. A variable is surrounded by curly quotes (e.g.,
variable 'i' gets referenced with '{i}'). When supplying multiple generators,
then these get treated as nested executions. Available generators: csv-file,
dirs, list, null, prompt, range, text-file
positional arguments:
pipeline The pipeline template with variables to expand and
then execute; see '--exec_format' option.
options:
-h, --help show this help message and exit
--exec_generator GENERATOR
The generator plugin(s) to use, incl. their options.
Flag needs to be specified for each generator.
(default: None)
--exec_dry_run Applies the generator to the pipeline template and
only outputs it on stdout. (default: False)
--exec_prefix PREFIX The string to prefix the pipeline with when in dry-run
mode. (default: None)
--exec_placeholders FILE
The file with custom placeholders to load (format:
key=value). (default: None)
--exec_format {cmdline,file}
The format that the pipeline is in. The format
'cmdline' interprets the remaining arguments as the
pipeline arguments to execute. The format 'file'
expects a file to load the pipeline arguments from.
This file format allows spreading the pipeline
arguments over multiple lines: it simply joins all
lines into a single command-line before splitting it
into individual arguments for execution. (default:
cmdline)
--exec_logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
The logging level to use. (default: WARN)
```
### Locating files
Readers tend to support input via file lists. The `idc-find` tool can generate
these.
```
usage: sdc-find [-h] -i DIR [DIR ...] [-r] -o FILE [-m [REGEXP ...]]
[-n [REGEXP ...]] [--split_ratios [SPLIT_RATIOS ...]]
[--split_names [SPLIT_NAMES ...]]
[--split_name_separator SPLIT_NAME_SEPARATOR]
[-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
Tool for locating files in directories that match certain patterns and store
them in files.
options:
-h, --help show this help message and exit
-i DIR [DIR ...], --input DIR [DIR ...]
The dir(s) to scan for files. (default: None)
-r, --recursive Whether to search the directories recursively
(default: False)
-o FILE, --output FILE
The file to store the located file names in (default:
None)
-m [REGEXP ...], --match [REGEXP ...]
The regular expression that the (full) file names must
match to be included (default: None)
-n [REGEXP ...], --not-match [REGEXP ...]
The regular expression that the (full) file names must
match to be excluded (default: None)
--split_ratios [SPLIT_RATIOS ...]
The split ratios to use for generating the splits
(int; must sum up to 100) (default: None)
--split_names [SPLIT_NAMES ...]
The split names to use as filename suffixes for the
generated splits (before .ext) (default: None)
--split_name_separator SPLIT_NAME_SEPARATOR
The separator to use between file name and split name
(default: -)
-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
The logging level to use. (default: WARN)
```
### Generating help screens for plugins
```
usage: sdc-help [-h] [-c [PACKAGE ...]] [-e EXCLUDED_CLASS_LISTERS]
[-T {pipeline,generator,cleaner}] [-p NAME]
[-f {text,markdown}] [-L INT] [-o PATH] [-i FILE] [-t TITLE]
[-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
Tool for outputting help for plugins in various formats.
options:
-h, --help show this help message and exit
-c [PACKAGE ...], --custom_class_listers [PACKAGE ...]
The custom class listers to use, uses the default ones
if not provided. (default: None)
-e EXCLUDED_CLASS_LISTERS, --excluded_class_listers EXCLUDED_CLASS_LISTERS
The comma-separated list of class listers to exclude.
(default: None)
-T {pipeline,generator,cleaner}, --plugin_type {pipeline,generator,cleaner}
The types of plugins to generate the help for.
(default: pipeline)
-p NAME, --plugin_name NAME
The name of the plugin to generate the help for,
generates it for all if not specified (default: None)
-f {text,markdown}, --help_format {text,markdown}
The output format to generate (default: text)
-L INT, --heading_level INT
The level to use for the heading (default: 1)
-o PATH, --output PATH
The directory or file to store the help in; outputs it
to stdout if not supplied; if pointing to a directory,
automatically generates file name from plugin name and
help format (default: None)
-i FILE, --index_file FILE
The file in the output directory to generate with an
overview of all plugins, grouped by type (in markdown
format, links them to the other generated files)
(default: None)
-t TITLE, --index_title TITLE
The title to use in the index file (default: spectral-
data-converter plugins)
-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
The logging level to use. (default: WARN)
```
### Plugin registry
```
usage: sdc-registry [-h] [-c CUSTOM_CLASS_LISTERS] [-e EXCLUDED_CLASS_LISTERS]
[-l {plugins,pipeline,custom-class-listers,env-class-listers,readers,direct-readers,filters,writers,direct-writers,generators,cleaners}]
For inspecting/querying the registry.
options:
-h, --help show this help message and exit
-c CUSTOM_CLASS_LISTERS, --custom_class_listers CUSTOM_CLASS_LISTERS
The comma-separated list of custom class listers to
use. (default: None)
-e EXCLUDED_CLASS_LISTERS, --excluded_class_listers EXCLUDED_CLASS_LISTERS
The comma-separated list of class listers to exclude.
(default: None)
-l {plugins,pipeline,custom-class-listers,env-class-listers,readers,direct-readers,filters,writers,direct-writers,generators,cleaners}, --list {plugins,pipeline,custom-class-listers,env-class-listers,readers,direct-readers,filters,writers,direct-writers,generators,cleaners}
For outputting various lists on stdout. (default:
None)
```
### Testing generators
```
usage: sdc-test-generator [-h] -g GENERATOR
[-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
Tool for testing generators by outputting the generated variables and their
associated values. Available generators: dirs, list, null, range
options:
-h, --help show this help message and exit
-g GENERATOR, --generator GENERATOR
The generator plugin to use. (default: None)
-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
The logging level to use. (default: WARN)
```
## Plugins
You can find help screens for the plugins here:
* [Pipeline plugins](plugins/README.md) (readers/filters/writers)
* [Generator plugins](generators/README.md) (used by `sdc-exec`)
* [Cleaner plugins](cleaners/README.md) (used by `apply-cleaner` filter)
## Class listers
The *spectral-data-converter* uses the *class lister registry* provided
by the [seppl](https://github.com/waikato-datamining/seppl) library.
Each module defines a function, typically called `list_classes` that returns
a dictionary of names of superclasses associated with a list of modules that
should be scanned for derived classes. Here is an example:
```python
from typing import List, Dict
def list_classes() -> Dict[str, List[str]]:
return {
"seppl.io.Reader": [
"mod.ule1",
"mod.ule2",
],
"seppl.io.Filter": [
"mod.ule3",
"mod.ule4",
],
"seppl.io.Writer": [
"mod.ule5",
],
}
```
Such a class lister gets referenced in the `entry_points` section of the `setup.py` file:
```python
entry_points={
"class_lister": [
"unique_string=module_name:function_name",
],
},
```
`:function_name` can be omitted if `:list_classes`.
The following environment variables can be used to influence the class listers:
* `SDC_CLASS_LISTERS`
* `SDC_CLASS_LISTERS_EXCL`
* `SDC_CLASS_LISTERS_IGNORED` - for class listers that provide ignored classes
Each variable is a comma-separated list of `module_name:function_name`, defining the class listers.
## Caching plugins
In order to speed up plugin discovery, they discovered plugins can be cached
on disk after the initial discovery. Installing additional plugins after
the cache has been initialized will not make them visible, the cache will
require resetting first.
The cache can be managed through the following environment variable:
```
SDC_CLASS_CACHE
```
It supports the following options:
* `off`: disables the cache
* `on`: enables the cache
* `reset`: resets the cached plugins first and enables the cache
## Additional libraries
* [Scikit-learn](https://github.com/waikato-datamining/image-dataset-converter-sklearn)
* [Visualizations](https://github.com/waikato-datamining/image-dataset-converter-vis)