agilent: For Agilent chromatograms
+Extractors for data files generated by various proprietary Agilent software.
+Extractor of Agilent OpenLab binary signal trace files (.ch and .it).
+Currently supports version “179” of the files. Version information is defined in
+the magic_values (parameters & metadata) and data_dtypes (data) dictionaries.
Adapted from ImportAgilent.m and +aston.
+Usage
+Available since yadg-4.0.
-
+
- +pydantic model dgbowl_schemas.yadg.dataschema_5_1.filetype.Agilent_ch +
- +
Show JSON schema
++{ + "title": "Agilent_ch", + "type": "object", + "properties": { + "filetype": { + "enum": [ + "agilent.ch", + "agilent-ch" + ], + "title": "Filetype", + "type": "string" + }, + "timezone": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Timezone" + }, + "locale": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Locale" + }, + "encoding": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Encoding" + }, + "parameters": { + "anyOf": [ + {}, + { + "type": "null" + } + ], + "default": null, + "title": "Parameters" + } + }, + "additionalProperties": false, + "required": [ + "filetype" + ] +} +
-
+
- Config: +
-
+
extra: str = forbid
+
+- Validators: +
-
+
- +
+
-
+
- +field filetype: Literal['agilent.ch', 'agilent-ch'] [Required] +
-
+
- Validated by: +
- + +
Schema
+datatree.DataTree:
+ {{ detector_name }}:
+ coords:
+ uts: !!float # Unix timestamp
+ elution_time: !!float # Elution time
+ data_vars:
+ signal: (uts, elution_time) # Signal data
+Metadata
+The following metadata is extracted:
++++
+- +
sampleid: Sample name.- +
username: User name used to generate the file.- +
method: Name of the chromatographic method.- +
version: Version of the CH file (only “179” is currently supported.)
Notes on file structure
+The following magic values are used: +.. code
+0x0000 "version magic"
+0x0108 "data offset"
+0x011a "x-axis minimum (ms)"
+0x011e "x-axis maximum (ms)"
+0x035a "sample ID"
+0x0559 "description"
+0x0758 "username"
+0x0957 "timestamp"
+0x09e5 "instrument name"
+0x09bc "inlet"
+0x0a0e "method"
+0x104c "y-axis unit"
+0x1075 "detector name"
+0x1274 "y-axis intercept"
+0x127c "y-axis slope"
+Data is stored in a consecutive set of <f8, starting at the offset (calculated
+as offset = ("data offset" - 1) * 512) until the end of the file.
Uncertainties
+Uncertainty in signal is the y-axis slope.
Uncertainty in elution_time is the x-axis step size.
Code author: Peter Kraus
+Extractor of Agilent Chemstation Chromtab tabulated data files. This file format may
+include multiple timesteps consisting of several traces each in a single CSV file. It
+contains a header section for each timestep, followed by a detector name, and a sequence
+of “X, Y” datapoints, which are stored as elution_time and signal.
Warning
+It is not guaranteed that the X-axis of the chromatogram (i.e. elution_time) is
+consistent between the timesteps of the same trace. The traces are expanded to the
+length of the longest trace, and the shorter traces are padded with NaNs.
Usage
+Available since yadg-4.0.
-
+
- +pydantic model dgbowl_schemas.yadg.dataschema_5_1.filetype.Agilent_csv +
- +
Show JSON schema
++{ + "title": "Agilent_csv", + "type": "object", + "properties": { + "filetype": { + "const": "agilent.csv", + "title": "Filetype" + }, + "timezone": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Timezone" + }, + "locale": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Locale" + }, + "encoding": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Encoding" + }, + "parameters": { + "anyOf": [ + {}, + { + "type": "null" + } + ], + "default": null, + "title": "Parameters" + } + }, + "additionalProperties": false, + "required": [ + "filetype" + ] +} +
-
+
- Config: +
-
+
extra: str = forbid
+
+- Validators: +
- +
-
+
- +field filetype: Literal['agilent.csv'] [Required] +
Schema
+datatree.DataTree:
+ {{ detector_name }}:
+ coords:
+ uts: !!float # Unix timestamp
+ elution_time: !!float # Elution time
+ data_vars:
+ signal: (uts, elution_time) # Signal data
+Metadata
+The following metadata is extracted:
++++
+- +
sampleid: Sample name.- +
datafile: Original path of the data file.
Uncertainties
+All uncertainties are derived from the string representation of the floats.
+Code author: Peter Kraus
+-
+
- +yadg.extractors.agilent.csv.extract(*, fn, encoding, timezone, **kwargs) +
-
+
- Return type: +
- + +
Extractor of Agilent OpenLab DX archives. This is a wrapper parser which unzips the
+provided DX file, and then uses the yadg.extractors.agilent.ch extractor
+to parse every CH file present in the archive. The IT files in the archive are currently
+ignored.
Note
+Currently the timesteps from multiple CH files (if present) are appended in the +timesteps array without any further sorting.
+Usage
+Available since yadg-4.0.
-
+
- +pydantic model dgbowl_schemas.yadg.dataschema_5_1.filetype.Agilent_ch +
- +
Show JSON schema
++{ + "title": "Agilent_ch", + "type": "object", + "properties": { + "filetype": { + "enum": [ + "agilent.ch", + "agilent-ch" + ], + "title": "Filetype", + "type": "string" + }, + "timezone": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Timezone" + }, + "locale": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Locale" + }, + "encoding": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Encoding" + }, + "parameters": { + "anyOf": [ + {}, + { + "type": "null" + } + ], + "default": null, + "title": "Parameters" + } + }, + "additionalProperties": false, + "required": [ + "filetype" + ] +} +
-
+
- Config: +
-
+
extra: str = forbid
+
+- Validators: +
- + +
-
+
- +field filetype: Literal['agilent.ch', 'agilent-ch'] [Required] +
-
+
- Validated by: +
- + +
-
+
- +field timezone: str | None = None +
-
+
- Validated by: +
-
+
timezone_resolve_localtime
+
+
-
+
- +field locale: str | None = None +
-
+
- Validated by: +
-
+
locale_set_default
+
+
-
+
- +field encoding: str | None = None +
-
+
- +field parameters: Any | None = None +
Schema
+datatree.DataTree:
+ {{ detector_name }}:
+ coords:
+ uts: !!float # Unix timestamp
+ elution_time: !!float # Elution time
+ data_vars:
+ signal: (uts, elution_time) # Signal data
+Metadata
+The following metadata is extracted:
++++
+- +
sampleid: Sample name.- +
username: User name used to generate the file.- +
method: Name of the chromatographic method.- +
version: Version of the CH file (only “179” is currently supported.)
Code author: Peter Kraus
+