brukeropus.file
The brukeropus.file submodule of brukeropus includes all the functions and classes for reading and exploring OPUS
files. This includes both high-level functions like read_opus that returns an OPUSFile class, as well as low-level
parsing functions like parse_directory that returns data extracted directly from the binary OPUS file bytes. This
overview documentation will focus on the high-level functions which will be useful for most users. If you are
interested in using the low-level parsing functions, perhaps to make your own data class or customize how files are
read, refer to: brukeropus.file.parse which contains all the low-level parsing functions.
Finding OPUS Files
OPUS files are typically saved with a numeric file extension (e.g. file.0, file.1, file.1001). This makes searching for
a list of OPUS files in a directory a little more cumbersome than a traditional "*.csv" search. To address this,
brukeropus includes a find_opus_files function:
from brukeropus import find_opus_files
filepaths = find_opus_files(r'path\to\opus\files', recursive=True)
Which will assign a list of filepaths that match the numeric extension formatting of OPUS files. For full documentation,
see brukeropus.file.utils.find_opus_files.
Reading OPUS Files
brukeropus parses OPUS files and assembles them into an OPUSFile object that contains the extracted data (and
metadata) within the file. You can generate an OPUSFile object in one of two ways:
from brukeropus import read_opus, OPUSFile
filepath = r'path\to\opusfile.0'
data = read_opus(filepath)
same_data = OPUSFile(filepath)
In the above code, data and same_data are both OPUSFile objects with identical data.
Using the OPUSFile Class
OPUS files all start with the same first four magic bytes. If the file does not start with these bytes (i.e. is not
a valid OPUS file), the OPUSFile class will logically evaluate to false:
data = read_opus('file.pdf')
if data:
print(data)
else:
print(data.filepath, 'is not an OPUS file')
The OPUSFile class provides an interface for accessing the data (stored as blocks) in an OPUS file. Accessible data
includes:
Parameters (brukeropus.file.params): measurement metadata
Data (brukeropus.file.data.Data): measurements spectra (1D)
DataSeries (brukeropus.file.data.DataSeries): series of measurements spectra (3D)
Report (brukeropus.file.report): tabular report info (e.g. multi-evaluation test reports)
To view a quick summary of the data contained in an OPUSFile instance, simply print it to the console:
data = read_opus('file.0')
print(data)
========================================================================================================================
OPUS File: file.0
Attribute Class type Description
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
params Parameters Optical, Fourier Transform, Acquisition, Sample Origin, Instrument Status Parameters
rf_params Parameters Instrument Status, Optical, Acquisition, Fourier Transform Reference Parameters
rf Data Reference Spectrum
igrf Data Reference Interferogram
a Data Absorbance
sm Data Sample Spectrum
phsm Data Sample Phase
igsm Data Sample Interferogram
history str History log of file
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
The output listed here will depend on what data blocks were saved in the OPUS file. The following sections will go over the various data class types in more detail.
Parameters (brukeropus.file.params.Parameters)
The metadata in an OPUS file is stored in Parameters classes. These classes can be stored in the params and
rf_params attributes which contain the sample and reference parameter metadata respectively.
To view all parameter metadata in the file, you can print to the console using the class method: print_parameters.
This will let you view all the key, value parameter data extracted from the file with labels for what the parameter keys
are referring to wherever known.
data = read_opus('file.0')
data.print_parameters()
Example
print_parameters Output
====================================================================================================
Sample/Result Parameters (params)
....................................................................................................
Optical Parameters
Key Label Value
ACC Accessory TRANS *010A984F
APR ATR Pressure 0
APT Aperture Setting 1 mm
BMS Beamsplitter KBr-Broadband
CHN Measurement Channel Sample Compartment
DTC Detector RT-DLaTGS [Internal Pos.1]
HPF High Pass Filter 0
LPF Low Pass Filter 10.0
LPV Variable Low Pass Filter (cm-1) 4000
OPF Optical Filter Setting Open
PGN Preamplifier Gain 3
RDX Extended Ready Check 0
SRC Source MIR
VEL Scanner Velocity 10.0
ADC External Analog Signals 0
SON External Sync Off
....................................................................................................
Fourier Transform Parameters
Key Label Value
APF Apodization Function B3
HFQ End Frequency Limit for File 500.0
LFQ Start Frequency Limit for File 10000.0
NLI Nonlinearity Correction 0
PHR Phase Resolution 100.0
PHZ Phase Correction Mode ML
SPZ Stored Phase Mode NO
ZFF Zero Filling Factor 2
....................................................................................................
Acquisition Parameters
Key Label Value
ADT Additional Data Treatment 0
AQM Acquisition Mode DD
CFE Low Intensity Power Mode with DTGS 0
COR Correlation Test Mode 0
DEL Delay Before Measurement 0
DLY Stabilization Delay 0
HFW Wanted High Freq Limit 15000.0
LFW Wanted Low Freq Limit 0.0
NSS Number of Sample Scans 50
PLF Result Spectrum Type AB
RES Resolution (cm-1) 4.0
SOT Sample Scans or Time 0
TCL Command Line for Additional Data Tr...
TDL To Do List 16777271
SGN Sample Signal Gain 1
....................................................................................................
Sample Origin Parameters
Key Label Value
BLD Building
CNM Operator Name Duran
CPY Company
DPM Department
EXP Experiment MWIR-LWIR_Trans_FileNameFormat.XPM
LCT Location
SFM Sample Form Atm-MWIR (All A)
SNM Sample Name File Test
XPP Experiment Path C:\Users\Public\Documents\Bruker\OPUS_8.1.29\XPM
IST Instrument Status OK
CPG Character Encoding Code Page 1252
UID Universally Unique Identifier 0d1348c2-3a2c-41c9-b521-bdaf0a23710c
....................................................................................................
Instrument Status Parameters
Key Label Value
HFL High Folding Limit 15795.820598
LFL Low Folding Limit 0.0
LWN Laser Wavenumber 15795.820598
ABP Absolute Peak Pos in Laser*2 52159
SSP Sample Spacing Divisor 1
ASG Actual Signal Gain 1
ARG Actual Reference Gain 1
ASS Number of Sample Scans 50
GFW Number of Good Forward Scans 25
GBW Number of Good Backward Scans 25
BFW Number of Bad Forward Scans 0
BBW Number of Bad Backward Scans 0
PKA Peak Amplitude 1409
PKL Peak Location 7364
PRA Backward Peak Amplitude 1356
PRL Backward Peak Location 7363
P2A Peak Amplitude Channel 2 1
P2L Peak Location Channel 2 1
P2R Backward Peak Amplitude Channel 2 1
P2K Backward Peak Location Channel 2 1
DAQ Data Acquisition Status 0
AG2 Actual Signal Gain Channel 2 1
HUM Relative Humidity Interferometer 14
SSM Sample Spacing Multiplier 1
RSN Running Sample Number 565
CRR Correlation Rejection Reason 0
SRT Start Time (sec) 1556890484.642
DUR Duration (sec) 42.433990478515625
TSC Scanner Temperature 27.8
MVD Max Velocity Deviation 0.1158025860786438
PRS Pressure Interferometer (hPa) 1009.9999700000001
AN1 Analog Signal 1 0.22596596493037535
AN2 Analog Signal 2 3.459206583321489
VSN Firmware Version 2.450 Oct 10 2014
SRN Instrument Serial Number 1135
CAM Coaddition Mode 0
INS Instrument Type VERTEX 80V
FOC Focal Length 100.0
RDY Ready Check 1
====================================================================================================
Reference Parameters (rf_params)
....................................................................................................
Reference Instrument Status Parameters
Key Label Value
HFL High Folding Limit 15795.820598
LFL Low Folding Limit 0.0
LWN Laser Wavenumber 15795.820598
ABP Absolute Peak Pos in Laser*2 52159
SSP Sample Spacing Divisor 1
ARG Actual Reference Gain 1
ASG Actual Signal Gain 1
ASS Number of Sample Scans 1
GFW Number of Good Forward Scans 1
GBW Number of Good Backward Scans 0
BFW Number of Bad Forward Scans 0
BBW Number of Bad Backward Scans 0
PKA Peak Amplitude 1644
PKL Peak Location 7364
PRA Backward Peak Amplitude 1
PRL Backward Peak Location -1
P2A Peak Amplitude Channel 2 1
P2L Peak Location Channel 2 1
P2R Backward Peak Amplitude Channel 2 1
P2K Backward Peak Location Channel 2 1
DAQ Data Acquisition Status 0
AG2 Actual Signal Gain Channel 2 1
HUM Relative Humidity Interferometer 0
SSM Sample Spacing Multiplier 1
RSN Running Sample Number 5816
CRR Correlation Rejection Reason 0
SRT Start Time (sec) 1556890282.358
DUR Duration (sec) 0.7919998168945312
TSC Scanner Temperature 27.8
MVD Max Velocity Deviation 0.10553144663572311
PRS Pressure Interferometer (hPa) 2.01999
AN1 Analog Signal 1 0.22577181458473206
AN2 Analog Signal 2 4.0960001945495605
VSN Firmware Version 2.450 Oct 10 2014
SRN Instrument Serial Number 1135
CAM Coaddition Mode 0
INS Instrument Type VERTEX 80V
FOC Focal Length 100.0
RDY Ready Check 1
ARS Number of Reference Scans 1
....................................................................................................
Reference Optical Parameters
Key Label Value
ACC Accessory TRANS *010A984F
APR ATR Pressure 0
APT Aperture Setting 1 mm
BMS Beamsplitter KBr-Broadband
DTC Detector RT-DLaTGS [Internal Pos.1]
HPF High Pass Filter 0
LPF Low Pass Filter 10.0
LPV Variable Low Pass Filter (cm-1) 4000
OPF Optical Filter Setting Open
PGR Reference Preamplifier Gain 3
RCH Reference Measurement Channel Sample Compartment
RDX Extended Ready Check 0
SRC Source MIR
VEL Scanner Velocity 10.0
ADC External Analog Signals 0
SON External Sync Off
....................................................................................................
Reference Acquisition Parameters
Key Label Value
ADT Additional Data Treatment 0
AQM Acquisition Mode DD
CFE Low Intensity Power Mode with DTGS 0
COR Correlation Test Mode 0
DEL Delay Before Measurement 0
DLY Stabilization Delay 0
HFW Wanted High Freq Limit 15000.0
LFW Wanted Low Freq Limit 0.0
NSR Number of Background Scans 1
PLF Result Spectrum Type TR
RES Resolution (cm-1) 4.0
RGN Reference Signal Gain 1
STR Scans or Time (Reference) 0
TCL Command Line for Additional Data Tr...
TDL To Do List 16777271
....................................................................................................
Reference Fourier Transform Parameters
Key Label Value
APF Apodization Function B3
HFQ End Frequency Limit for File 500.0
LFQ Start Frequency Limit for File 10000.0
NLI Nonlinearity Correction 0
PHR Phase Resolution 100.0
PHZ Phase Correction Mode ML
SPZ Stored Phase Mode NO
ZFF Zero Filling Factor 2
You can access the sample parameters through the OPUSFile.params attribute, or as a direct attribute for shorthand
(e.g. OPUSFile.params.apt or OPUSFile.apt). The parameter keys are also case insensitive (e.g. OPUSFile.bms or
OPUSFile.BMS).
OPUS files can also contain parameter information about the associated reference (aka background) measurement. These
parameters are only accessible through the OPUSFile.rf_params attribute to avoid namespace collisions (e.g.
OPUSFile.rf_params.apt).
data = read_opus('file.0')
print('Sample ZFF:', data.zff, 'Reference ZFF:', data.rf_params.zff)
Sample ZFF: 2 Reference ZFF: 2
You can also get the human-readable label for a parameter key using the get_param_label function:
from brukeropus.file import get_param_label
data = read_opus('file.0')
print(get_param_label('bms') + ':', data.bms)
print(get_param_label('src') + ':', data.src)
Beamsplitter: KBr-Broadband
Source: MIR
You can also iterate over the parameters using the familiar keys(), values(), and items() functions using the
params or rf_params attributes (just like a dictionary):
data = read_opus('file.0')
for key, val in data.params.items():
print(key + ':', val)
acc: TRANS *010A984F
apr: 0
apt: 1 mm
bms: KBr-Broadband
chn: Sample Compartment
dtc: RT-DLaTGS [Internal Pos.1]
hpf: 0
lpf: 10.0
lpv: 4000
opf: Open
pgn: 3
... continued ...
Data and DataSeries (brukeropus.file.data)
Depending on the settings used to save the OPUS file, different data blocks can be stored. These can include phase,
interferograms, single-channel spectra and result spectra (e.g. absorbance, transmittance, etc.). To retrieve a list of
the data blocks stored in the OPUS File, you can use the all_data_keys attribute:
data = read_opus('file.0')
print(data.all_data_keys)
['igsm', 'phsm', 'sm', 'a', 'igrf', 'rf']
Each key is also an attribute of the OPUSFile instance that returns either a Data (single spectra) or DataSeries
(series of spectra) class. You can use the data_keys attribute to retrieve a list of only the single-spectra Data
keys in the class, or the series_keys attribute to retrieve a list of only the DataSeries keys.
You can also iterate over these data keys using the iter_all_data(), iter_data() and iter_series() class
methods:
data = read_opus('file.0')
for d in data.iter_data():
print(d.label, '(' + d.datetime.isoformat(' ') + ')')
Sample Interferogram (2019-05-03 13:34:44.641000)
Sample Phase (2019-05-03 13:34:44.641000)
Sample Spectrum (2019-05-03 13:34:44.641000)
Absorbance (2019-05-03 13:34:44.641000)
Reference Interferogram (2019-05-03 13:31:22.358000)
Reference Spectrum (2019-05-03 13:31:22.358000)
You can access the x and y arrays of a Data or DataSeries class:
data = read_opus('file.0')
plt.plot(data.a.x, data.a.y) # Plot absorbance
plt.ylim((0, 1))
plt.show()
For spectra with wavenumber as valid unit (e.g. single-channel or result spectra), the x array can be given in
wavenumber [cm⁻¹], wavelength [µm], or modulation frequency [Hz] units by using the attributes: wn, wl, or f
respectively:
data = read_opus('file.0')
plt.plot(data.sm.wl, data.sm.y)
plt.show()
Each data block in an OPUS file also contains a small parameter block with information such as the min/max y-value
(mny, mxy), x-units (dxu), number of data points (npt), etc. These can be accessed as direct attributes to the Data
class, or through the Data.params attribute:
data = read_opus('file.0')
print('Sample spectra y-min:', data.sm.mny, 'y-max:', data.sm.mxy)
Sample spectra y-min: 1.2147593224653974e-05 y-max: 0.03543896973133087
Reports (brukeropus.file.report)
OPUS files may also store a variety of reports which typically contain data in tabular format. Because an OPUS file may
contain multiple reports, they are stored as a list in the reports attribute (even if only one is available). For
OPUS files with no reports, the reports attribute will simply return an empty list. Reports can be printed to the
console. As an example of how to access the report data, we will use a Multi-Evaluation Test Report (mev):
data = read_opus(mevfile.0)
print(data.reports[0])
====================================================================================================
Multi Evaluation Test Report
____________________________________________________________________________________________________
Version: 4
Method Path: C:\Users\Public\Documents\Bruker\OPUS_8.9.7\ME_Base\ME
Method Name: IPA Water Int Q1 Q2.mev
Method Date Time: 2025/04/03 17:39:01 (GMT-5)
Multi Evaluation Test Report (table): cols: 6, rows: 4
----------------------------------------------------------------------------------------------------
Type: Q2 Q2 INT INT Q1 Q1
Subreport: 1 1 2 2 3 3
Row: 1 2 1 2 1 2
Last Change: 0 0 0 0 0 0
----------------------------------------------------------------------------------------------------
Subreport 0
Quant 2 (table): cols: 2, rows: 35
----------------------------------------------------------------------------------------------------
Method_Path: C:\Users\Public\Docume... C:\Users\Public\Docume...
Method_Name: IPA Method.q2 H2O Method.q2
Date_Time_Method: 2025/04/03 11:50:33 (G... 2025/04/03 11:47:05 (G...
Date_Time_Analysis: 2025/04/03 21:26:08 (G... 2025/04/03 21:26:09 (G...
X_Startpoint: 8920 9900
X_Endpoint: 5396 6028
Component_Name: IPA H2O
Component_Unit: % %
Component_Name_User: IPA H2O
Component_Unit_User: % %
Formatting: %.5G %.5G
Prediction: -0.0157854 100.162
Prediction_Outside: 1 1
Prediction_Calculated: -0.0157854 100.162
Prediction_Calculated_Outside: 0 0
Formula:
External_Bias: 3.40282e+38 3.40282e+38
Target_Concentration: 3.40282e+38 3.40282e+38
Warning_Upper_Limit: 3.40282e+38 3.40282e+38
Warning_Lower_Limit: 3.40282e+38 3.40282e+38
Alarm_Upper_Limit: 3.40282e+38 3.40282e+38
Alarm_Lower_Limit: 3.40282e+38 3.40282e+38
Mah_Dist: 0.281401 0.330205
Mah_Dist_Limit: 0.569619 0.717409
Mah_Dist_Limit_By_Factor: 0.569619 0.717409
Mah_Dist_Outlier: 0 0
MDI: 0.494015 0.460275
Spec_Residual: 0.000657344 0.000157652
F_Value: 1.78523 0.977421
F_Prob: 0.801844 0.664059
F_Prob_Limit: 0.99 0.99
Spec_Residual_Outlier: 0 0
Component_Value_Density: 3.40282e+38 3.40282e+38
Component_Value_Density_Limit: 3.40282e+38 3.40282e+38
Process_Channel_Name:
----------------------------------------------------------------------------------------------------
Subreport 1
Integration (table): cols: 2, rows: 25
----------------------------------------------------------------------------------------------------
Method_Path: C:\Users\Public\Docume... C:\Users\Public\Docume...
Method_Name: Water Integration.int IPA Integration.int
Date_Time_Method: 2025/04/03 12:49:06 (G... 2025/04/03 12:45:18 (G...
Date_Time_Analysis: 2025/04/03 21:26:09 (G... 2025/04/03 21:26:09 (G...
X_Startpoint: 8127.6 5970.95
X_Endpoint: 7368.4 5874.2
Label: H2O IPA
Label_User: H2O IPA
Type: B B
Formatting: %.6G %.6G
Integration_Result: -155.238 -0.918539
Integration_Result_Calculated: -155.238 -0.918539
Formula:
Freq_1: 8127.6 5970.95
Freq_2: 7368.4 5874.2
Freq_3: 1.001e-199 1.001e-199
Freq_4: 1.001e-199 1.001e-199
Freq_5: 1.001e-199 1.001e-199
Freq_6: 1.001e-199 1.001e-199
Target_Concentration: 3.40282e+38 3.40282e+38
Warning_Upper_Limit: 3.40282e+38 3.40282e+38
Warning_Lower_Limit: 3.40282e+38 3.40282e+38
Alarm_Upper_Limit: 3.40282e+38 3.40282e+38
Alarm_Lower_Limit: 3.40282e+38 3.40282e+38
Process_Channel_Name:
----------------------------------------------------------------------------------------------------
Subreport 2
Quant 1 (table): cols: 2, rows: 22
----------------------------------------------------------------------------------------------------
Method_Path: C:\Users\Public\Docume... C:\Users\Public\Docume...
Method_Name: Water Quant 1_Linear.q1 IPA Quant 1_Linear.q1
Date_Time_Method: 2025/04/03 12:48:16 (G... 2025/04/03 09:03:49 (G...
Date_Time_Analysis: 2025/04/03 21:26:09 (G... 2025/04/03 21:26:09 (G...
X_Startpoint: 7368.4 5874.2
X_Endpoint: 8127.6 5970.95
Component_Name: Water IPA
Component_Unit: % %
Component_Name_User: Water IPA
Component_Unit_User: % %
Formatting: %.4G %.4G
Prediction: 86.3654 -7.54551
Prediction_Calculated: 86.3654 -7.54551
Formula:
Sigma: 9.65275 10.7219
Integration_Result: 159.336 135.308
Target_Concentration: 3.40282e+38 3.40282e+38
Warning_Upper_Limit: 3.40282e+38 3.40282e+38
Warning_Lower_Limit: 3.40282e+38 3.40282e+38
Alarm_Upper_Limit: 3.40282e+38 3.40282e+38
Alarm_Lower_Limit: 3.40282e+38 3.40282e+38
Process_Channel_Name:
----------------------------------------------------------------------------------------------------
====================================================================================================
At the very top of the report, you see a centered title. This title can be accessed by the title
attribute of the Report.
report = data.reports[0]
print(report.title)
Multi Evaluation Test Report
After the title, you see a list of report properties. These properties are stored as a dict in
the properties attribute of a Report, but can also be accessed by indexing the report using the
property key (case insensitive):
for key, val in report.properties.items():
print(key, val)
print('\nAccessing report properties by name:')
print(report['Method Name'], report['Method Name'] == report['method name'])
Version 4
Method Path C:\Users\Public\Documents\Bruker\OPUS_8.9.7\ME_Base\ME
Method Name IPA Water Int Q1 Q2.mev
Method Date Time 2025/04/03 17:39:01 (GMT-5)
Accessing report properties by name:
IPA Water Int Q1 Q2.mev True
Following the report properties is a table. This data is stored in the table attribute of a
Report as a ReportTable class (brukeropus.file.report.ReportTable). ReportTables have
titles, headers, and values. Below is a snippet showing how to access data from the report table:
print('Table title:', report.table.title)
print('Table Headers:', report.table.header)
print('Table row values by name:', report.table['Type'])
print('Table row values by index:', report.table[1])
print('Last value of a table row:', report.table['Type'][-1])
Table title: Multi Evaluation Test Report
Table Headers: ['Type', 'Subreport', 'Row', 'Last Change']
Table row values by name: ['Q2', 'Q2', 'INT', 'INT', 'Q1', 'Q1']
Table row values by index: [1, 1, 2, 2, 3, 3]
Last value of a table row: Q1
In this report, the table is followed by a series of subreports. Because a report can have multiple
subreports (this file has 3), they are stored as a list in the sub attribute of a Report.
Subreports can be accessed by indexing the sub attribute, or directly indexing the Report.
Because these subreports are ReportTables, they have the same interface as above:
print('First subreport title:', report.sub[0].title)
print('Second subreport title:', report[1].title)
print('First subreport Method Names:', report[0]['method_name'])
print('First method name of the first subreport:', report[0]['method_name'][0])
First subreport title: Quant 2
Second subreport title: Integration
First subreport Method Names: ['IPA Method.q2', 'H2O Method.q2']
First method name of the first subreport: IPA Method.q2
1''' 2The `brukeropus.file` submodule of `brukeropus` includes all the functions and classes for reading and exploring OPUS 3files. This includes both high-level functions like `read_opus` that returns an `OPUSFile` class, as well as low-level 4parsing functions like `parse_directory` that returns data extracted directly from the binary OPUS file bytes. This 5overview documentation will focus on the high-level functions which will be useful for most users. If you are 6interested in using the low-level parsing functions, perhaps to make your own data class or customize how files are 7read, refer to: `brukeropus.file.parse` which contains all the low-level parsing functions. 8## Finding OPUS Files 9OPUS files are typically saved with a numeric file extension (e.g. file.0, file.1, file.1001). This makes searching for 10a list of OPUS files in a directory a little more cumbersome than a traditional "*.csv" search. To address this, 11`brukeropus` includes a `find_opus_files` function: 12```python 13from brukeropus import find_opus_files 14 15filepaths = find_opus_files(r'path\\to\\opus\\files', recursive=True) 16``` 17Which will assign a list of filepaths that match the numeric extension formatting of OPUS files. For full documentation, 18see `brukeropus.file.utils.find_opus_files`. 19## Reading OPUS Files 20`brukeropus` parses OPUS files and assembles them into an `OPUSFile` object that contains the extracted data (and 21metadata) within the file. You can generate an `OPUSFile` object in one of two ways: 22```python 23from brukeropus import read_opus, OPUSFile 24 25filepath = r'path\\to\\opusfile.0' 26 27data = read_opus(filepath) 28same_data = OPUSFile(filepath) 29``` 30In the above code, `data` and `same_data` are both `OPUSFile` objects with identical data. 31## Using the `OPUSFile` Class 32OPUS files all start with the same first four *magic bytes*. If the file does not start with these bytes (i.e. is not 33a valid OPUS file), the `OPUSFile` class will logically evaluate to `false`: 34```python 35data = read_opus('file.pdf') 36if data: 37 print(data) 38else: 39 print(data.filepath, 'is not an OPUS file') 40``` 41The `OPUSFile` class provides an interface for accessing the data (stored as blocks) in an OPUS file. Accessible data 42includes: 43 44**Parameters** (`brukeropus.file.params`): measurement metadata 45 46**Data** (`brukeropus.file.data.Data`): measurements spectra (1D) 47 48**DataSeries** (`brukeropus.file.data.DataSeries`): series of measurements spectra (3D) 49 50**Report** (`brukeropus.file.report`): tabular report info (e.g. multi-evaluation test reports) 51 52To view a quick summary of the data contained in an `OPUSFile` instance, simply print it to the console: 53 54```python 55data = read_opus('file.0') 56print(data) 57``` 58```console 59======================================================================================================================== 60 OPUS File: file.0 61Attribute Class type Description 62―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 63params Parameters Optical, Fourier Transform, Acquisition, Sample Origin, Instrument Status Parameters 64rf_params Parameters Instrument Status, Optical, Acquisition, Fourier Transform Reference Parameters 65rf Data Reference Spectrum 66igrf Data Reference Interferogram 67a Data Absorbance 68sm Data Sample Spectrum 69phsm Data Sample Phase 70igsm Data Sample Interferogram 71history str History log of file 72―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 73``` 74The output listed here will depend on what data blocks were saved in the OPUS file. The following sections will go 75over the various data class types in more detail. 76 77###Parameters (brukeropus.file.params.Parameters) 78 79The metadata in an OPUS file is stored in `Parameters` classes. These classes can be stored in the `params` and 80`rf_params` attributes which contain the sample and reference parameter metadata respectively. 81 82To view all parameter metadata in the file, you can print to the console using the class method: `print_parameters`. 83This will let you view all the key, value parameter data extracted from the file with labels for what the parameter keys 84are referring to wherever known. 85 86```python 87data = read_opus('file.0') 88data.print_parameters() 89``` 90<details> 91<summary>Example `print_parameters` Output</summary> 92<p> 93```console 94==================================================================================================== 95 Sample/Result Parameters (params) 96 97.................................................................................................... 98 Optical Parameters 99Key Label Value 100ACC Accessory TRANS *010A984F 101APR ATR Pressure 0 102APT Aperture Setting 1 mm 103BMS Beamsplitter KBr-Broadband 104CHN Measurement Channel Sample Compartment 105DTC Detector RT-DLaTGS [Internal Pos.1] 106HPF High Pass Filter 0 107LPF Low Pass Filter 10.0 108LPV Variable Low Pass Filter (cm-1) 4000 109OPF Optical Filter Setting Open 110PGN Preamplifier Gain 3 111RDX Extended Ready Check 0 112SRC Source MIR 113VEL Scanner Velocity 10.0 114ADC External Analog Signals 0 115SON External Sync Off 116 117.................................................................................................... 118 Fourier Transform Parameters 119Key Label Value 120APF Apodization Function B3 121HFQ End Frequency Limit for File 500.0 122LFQ Start Frequency Limit for File 10000.0 123NLI Nonlinearity Correction 0 124PHR Phase Resolution 100.0 125PHZ Phase Correction Mode ML 126SPZ Stored Phase Mode NO 127ZFF Zero Filling Factor 2 128 129.................................................................................................... 130 Acquisition Parameters 131Key Label Value 132ADT Additional Data Treatment 0 133AQM Acquisition Mode DD 134CFE Low Intensity Power Mode with DTGS 0 135COR Correlation Test Mode 0 136DEL Delay Before Measurement 0 137DLY Stabilization Delay 0 138HFW Wanted High Freq Limit 15000.0 139LFW Wanted Low Freq Limit 0.0 140NSS Number of Sample Scans 50 141PLF Result Spectrum Type AB 142RES Resolution (cm-1) 4.0 143SOT Sample Scans or Time 0 144TCL Command Line for Additional Data Tr... 145TDL To Do List 16777271 146SGN Sample Signal Gain 1 147 148.................................................................................................... 149 Sample Origin Parameters 150Key Label Value 151BLD Building 152CNM Operator Name Duran 153CPY Company 154DPM Department 155EXP Experiment MWIR-LWIR_Trans_FileNameFormat.XPM 156LCT Location 157SFM Sample Form Atm-MWIR (All A) 158SNM Sample Name File Test 159XPP Experiment Path C:\\Users\\Public\\Documents\\Bruker\\OPUS_8.1.29\\XPM 160IST Instrument Status OK 161CPG Character Encoding Code Page 1252 162UID Universally Unique Identifier 0d1348c2-3a2c-41c9-b521-bdaf0a23710c 163 164.................................................................................................... 165 Instrument Status Parameters 166Key Label Value 167HFL High Folding Limit 15795.820598 168LFL Low Folding Limit 0.0 169LWN Laser Wavenumber 15795.820598 170ABP Absolute Peak Pos in Laser*2 52159 171SSP Sample Spacing Divisor 1 172ASG Actual Signal Gain 1 173ARG Actual Reference Gain 1 174ASS Number of Sample Scans 50 175GFW Number of Good Forward Scans 25 176GBW Number of Good Backward Scans 25 177BFW Number of Bad Forward Scans 0 178BBW Number of Bad Backward Scans 0 179PKA Peak Amplitude 1409 180PKL Peak Location 7364 181PRA Backward Peak Amplitude 1356 182PRL Backward Peak Location 7363 183P2A Peak Amplitude Channel 2 1 184P2L Peak Location Channel 2 1 185P2R Backward Peak Amplitude Channel 2 1 186P2K Backward Peak Location Channel 2 1 187DAQ Data Acquisition Status 0 188AG2 Actual Signal Gain Channel 2 1 189HUM Relative Humidity Interferometer 14 190SSM Sample Spacing Multiplier 1 191RSN Running Sample Number 565 192CRR Correlation Rejection Reason 0 193SRT Start Time (sec) 1556890484.642 194DUR Duration (sec) 42.433990478515625 195TSC Scanner Temperature 27.8 196MVD Max Velocity Deviation 0.1158025860786438 197PRS Pressure Interferometer (hPa) 1009.9999700000001 198AN1 Analog Signal 1 0.22596596493037535 199AN2 Analog Signal 2 3.459206583321489 200VSN Firmware Version 2.450 Oct 10 2014 201SRN Instrument Serial Number 1135 202CAM Coaddition Mode 0 203INS Instrument Type VERTEX 80V 204FOC Focal Length 100.0 205RDY Ready Check 1 206 207==================================================================================================== 208 Reference Parameters (rf_params) 209 210.................................................................................................... 211 Reference Instrument Status Parameters 212Key Label Value 213HFL High Folding Limit 15795.820598 214LFL Low Folding Limit 0.0 215LWN Laser Wavenumber 15795.820598 216ABP Absolute Peak Pos in Laser*2 52159 217SSP Sample Spacing Divisor 1 218ARG Actual Reference Gain 1 219ASG Actual Signal Gain 1 220ASS Number of Sample Scans 1 221GFW Number of Good Forward Scans 1 222GBW Number of Good Backward Scans 0 223BFW Number of Bad Forward Scans 0 224BBW Number of Bad Backward Scans 0 225PKA Peak Amplitude 1644 226PKL Peak Location 7364 227PRA Backward Peak Amplitude 1 228PRL Backward Peak Location -1 229P2A Peak Amplitude Channel 2 1 230P2L Peak Location Channel 2 1 231P2R Backward Peak Amplitude Channel 2 1 232P2K Backward Peak Location Channel 2 1 233DAQ Data Acquisition Status 0 234AG2 Actual Signal Gain Channel 2 1 235HUM Relative Humidity Interferometer 0 236SSM Sample Spacing Multiplier 1 237RSN Running Sample Number 5816 238CRR Correlation Rejection Reason 0 239SRT Start Time (sec) 1556890282.358 240DUR Duration (sec) 0.7919998168945312 241TSC Scanner Temperature 27.8 242MVD Max Velocity Deviation 0.10553144663572311 243PRS Pressure Interferometer (hPa) 2.01999 244AN1 Analog Signal 1 0.22577181458473206 245AN2 Analog Signal 2 4.0960001945495605 246VSN Firmware Version 2.450 Oct 10 2014 247SRN Instrument Serial Number 1135 248CAM Coaddition Mode 0 249INS Instrument Type VERTEX 80V 250FOC Focal Length 100.0 251RDY Ready Check 1 252ARS Number of Reference Scans 1 253 254.................................................................................................... 255 Reference Optical Parameters 256Key Label Value 257ACC Accessory TRANS *010A984F 258APR ATR Pressure 0 259APT Aperture Setting 1 mm 260BMS Beamsplitter KBr-Broadband 261DTC Detector RT-DLaTGS [Internal Pos.1] 262HPF High Pass Filter 0 263LPF Low Pass Filter 10.0 264LPV Variable Low Pass Filter (cm-1) 4000 265OPF Optical Filter Setting Open 266PGR Reference Preamplifier Gain 3 267RCH Reference Measurement Channel Sample Compartment 268RDX Extended Ready Check 0 269SRC Source MIR 270VEL Scanner Velocity 10.0 271ADC External Analog Signals 0 272SON External Sync Off 273 274.................................................................................................... 275 Reference Acquisition Parameters 276Key Label Value 277ADT Additional Data Treatment 0 278AQM Acquisition Mode DD 279CFE Low Intensity Power Mode with DTGS 0 280COR Correlation Test Mode 0 281DEL Delay Before Measurement 0 282DLY Stabilization Delay 0 283HFW Wanted High Freq Limit 15000.0 284LFW Wanted Low Freq Limit 0.0 285NSR Number of Background Scans 1 286PLF Result Spectrum Type TR 287RES Resolution (cm-1) 4.0 288RGN Reference Signal Gain 1 289STR Scans or Time (Reference) 0 290TCL Command Line for Additional Data Tr... 291TDL To Do List 16777271 292 293.................................................................................................... 294 Reference Fourier Transform Parameters 295Key Label Value 296APF Apodization Function B3 297HFQ End Frequency Limit for File 500.0 298LFQ Start Frequency Limit for File 10000.0 299NLI Nonlinearity Correction 0 300PHR Phase Resolution 100.0 301PHZ Phase Correction Mode ML 302SPZ Stored Phase Mode NO 303ZFF Zero Filling Factor 2 304``` 305</p> 306</details> 307 308You can access the sample parameters through the `OPUSFile.params` attribute, or as a direct attribute for shorthand 309(e.g. `OPUSFile.params.apt` or `OPUSFile.apt`). The parameter keys are also case insensitive (e.g. `OPUSFile.bms` or 310`OPUSFile.BMS`). 311 312OPUS files can also contain parameter information about the associated reference (aka background) measurement. These 313parameters are only accessible through the `OPUSFile.rf_params` attribute to avoid namespace collisions (e.g. 314`OPUSFile.rf_params.apt`). 315 316```python 317data = read_opus('file.0') 318print('Sample ZFF:', data.zff, 'Reference ZFF:', data.rf_params.zff) 319``` 320```console 321Sample ZFF: 2 Reference ZFF: 2 322``` 323 324You can also get the human-readable label for a parameter key using the `get_param_label` function: 325 326```python 327from brukeropus.file import get_param_label 328data = read_opus('file.0') 329print(get_param_label('bms') + ':', data.bms) 330print(get_param_label('src') + ':', data.src) 331``` 332```console 333Beamsplitter: KBr-Broadband 334Source: MIR 335``` 336 337You can also iterate over the parameters using the familiar `keys()`, `values()`, and `items()` functions using the 338`params` or `rf_params` attributes (just like a dictionary): 339 340```python 341data = read_opus('file.0') 342for key, val in data.params.items(): 343 print(key + ':', val) 344``` 345```console 346acc: TRANS *010A984F 347apr: 0 348apt: 1 mm 349bms: KBr-Broadband 350chn: Sample Compartment 351dtc: RT-DLaTGS [Internal Pos.1] 352hpf: 0 353lpf: 10.0 354lpv: 4000 355opf: Open 356pgn: 3 357... continued ... 358``` 359 360###Data and DataSeries (brukeropus.file.data) 361 362Depending on the settings used to save the OPUS file, different data blocks can be stored. These can include phase, 363interferograms, single-channel spectra and result spectra (e.g. absorbance, transmittance, etc.). To retrieve a list of 364the data blocks stored in the OPUS File, you can use the `all_data_keys` attribute: 365 366```python 367data = read_opus('file.0') 368print(data.all_data_keys) 369``` 370```console 371['igsm', 'phsm', 'sm', 'a', 'igrf', 'rf'] 372``` 373 374Each key is also an attribute of the `OPUSFile` instance that returns either a `Data` (single spectra) or `DataSeries` 375(series of spectra) class. You can use the `data_keys` attribute to retrieve a list of only the single-spectra `Data` 376keys in the class, or the `series_keys` attribute to retrieve a list of only the `DataSeries` keys. 377 378You can also iterate over these data keys using the `iter_all_data()`, `iter_data()` and `iter_series()` class 379methods: 380 381```python 382data = read_opus('file.0') 383for d in data.iter_data(): 384 print(d.label, '(' + d.datetime.isoformat(' ') + ')') 385``` 386```console 387Sample Interferogram (2019-05-03 13:34:44.641000) 388Sample Phase (2019-05-03 13:34:44.641000) 389Sample Spectrum (2019-05-03 13:34:44.641000) 390Absorbance (2019-05-03 13:34:44.641000) 391Reference Interferogram (2019-05-03 13:31:22.358000) 392Reference Spectrum (2019-05-03 13:31:22.358000) 393``` 394 395You can access the `x` and `y` arrays of a `Data` or `DataSeries` class: 396 397```python 398data = read_opus('file.0') 399plt.plot(data.a.x, data.a.y) # Plot absorbance 400plt.ylim((0, 1)) 401plt.show() 402``` 403 404For spectra with wavenumber as valid unit (e.g. single-channel or result spectra), the `x` array can be given in 405wavenumber [`cm⁻¹`], wavelength [`µm`], or modulation frequency [`Hz`] units by using the attributes: `wn`, `wl`, or `f` 406respectively: 407 408```python 409data = read_opus('file.0') 410plt.plot(data.sm.wl, data.sm.y) 411plt.show() 412``` 413 414Each data block in an OPUS file also contains a small parameter block with information such as the min/max y-value 415(mny, mxy), x-units (dxu), number of data points (npt), etc. These can be accessed as direct attributes to the `Data` 416class, or through the `Data.params` attribute: 417 418```python 419data = read_opus('file.0') 420print('Sample spectra y-min:', data.sm.mny, 'y-max:', data.sm.mxy) 421``` 422```console 423Sample spectra y-min: 1.2147593224653974e-05 y-max: 0.03543896973133087 424``` 425 426###Reports (brukeropus.file.report) 427 428OPUS files may also store a variety of reports which typically contain data in tabular format. Because an OPUS file may 429contain multiple reports, they are stored as a `list` in the `reports` attribute (even if only one is available). For 430OPUS files with no reports, the `reports` attribute will simply return an empty list. Reports can be printed to the 431console. As an example of how to access the report data, we will use a Multi-Evaluation Test Report (mev): 432 433```python 434data = read_opus(mevfile.0) 435print(data.reports[0]) 436``` 437 438```console 439==================================================================================================== 440 Multi Evaluation Test Report 441____________________________________________________________________________________________________ 442 Version: 4 443 Method Path: C:\\Users\\Public\\Documents\\Bruker\\OPUS_8.9.7\\ME_Base\ME 444 Method Name: IPA Water Int Q1 Q2.mev 445Method Date Time: 2025/04/03 17:39:01 (GMT-5) 446 447 448Multi Evaluation Test Report (table): cols: 6, rows: 4 449---------------------------------------------------------------------------------------------------- 450 Type: Q2 Q2 INT INT Q1 Q1 451 Subreport: 1 1 2 2 3 3 452 Row: 1 2 1 2 1 2 453Last Change: 0 0 0 0 0 0 454---------------------------------------------------------------------------------------------------- 455Subreport 0 456Quant 2 (table): cols: 2, rows: 35 457---------------------------------------------------------------------------------------------------- 458 Method_Path: C:\\Users\\Public\\Docume... C:\\Users\\Public\\Docume... 459 Method_Name: IPA Method.q2 H2O Method.q2 460 Date_Time_Method: 2025/04/03 11:50:33 (G... 2025/04/03 11:47:05 (G... 461 Date_Time_Analysis: 2025/04/03 21:26:08 (G... 2025/04/03 21:26:09 (G... 462 X_Startpoint: 8920 9900 463 X_Endpoint: 5396 6028 464 Component_Name: IPA H2O 465 Component_Unit: % % 466 Component_Name_User: IPA H2O 467 Component_Unit_User: % % 468 Formatting: %.5G %.5G 469 Prediction: -0.0157854 100.162 470 Prediction_Outside: 1 1 471 Prediction_Calculated: -0.0157854 100.162 472Prediction_Calculated_Outside: 0 0 473 Formula: 474 External_Bias: 3.40282e+38 3.40282e+38 475 Target_Concentration: 3.40282e+38 3.40282e+38 476 Warning_Upper_Limit: 3.40282e+38 3.40282e+38 477 Warning_Lower_Limit: 3.40282e+38 3.40282e+38 478 Alarm_Upper_Limit: 3.40282e+38 3.40282e+38 479 Alarm_Lower_Limit: 3.40282e+38 3.40282e+38 480 Mah_Dist: 0.281401 0.330205 481 Mah_Dist_Limit: 0.569619 0.717409 482 Mah_Dist_Limit_By_Factor: 0.569619 0.717409 483 Mah_Dist_Outlier: 0 0 484 MDI: 0.494015 0.460275 485 Spec_Residual: 0.000657344 0.000157652 486 F_Value: 1.78523 0.977421 487 F_Prob: 0.801844 0.664059 488 F_Prob_Limit: 0.99 0.99 489 Spec_Residual_Outlier: 0 0 490 Component_Value_Density: 3.40282e+38 3.40282e+38 491Component_Value_Density_Limit: 3.40282e+38 3.40282e+38 492 Process_Channel_Name: 493---------------------------------------------------------------------------------------------------- 494Subreport 1 495Integration (table): cols: 2, rows: 25 496---------------------------------------------------------------------------------------------------- 497 Method_Path: C:\\Users\\Public\\Docume... C:\\Users\\Public\\Docume... 498 Method_Name: Water Integration.int IPA Integration.int 499 Date_Time_Method: 2025/04/03 12:49:06 (G... 2025/04/03 12:45:18 (G... 500 Date_Time_Analysis: 2025/04/03 21:26:09 (G... 2025/04/03 21:26:09 (G... 501 X_Startpoint: 8127.6 5970.95 502 X_Endpoint: 7368.4 5874.2 503 Label: H2O IPA 504 Label_User: H2O IPA 505 Type: B B 506 Formatting: %.6G %.6G 507 Integration_Result: -155.238 -0.918539 508Integration_Result_Calculated: -155.238 -0.918539 509 Formula: 510 Freq_1: 8127.6 5970.95 511 Freq_2: 7368.4 5874.2 512 Freq_3: 1.001e-199 1.001e-199 513 Freq_4: 1.001e-199 1.001e-199 514 Freq_5: 1.001e-199 1.001e-199 515 Freq_6: 1.001e-199 1.001e-199 516 Target_Concentration: 3.40282e+38 3.40282e+38 517 Warning_Upper_Limit: 3.40282e+38 3.40282e+38 518 Warning_Lower_Limit: 3.40282e+38 3.40282e+38 519 Alarm_Upper_Limit: 3.40282e+38 3.40282e+38 520 Alarm_Lower_Limit: 3.40282e+38 3.40282e+38 521 Process_Channel_Name: 522---------------------------------------------------------------------------------------------------- 523Subreport 2 524Quant 1 (table): cols: 2, rows: 22 525---------------------------------------------------------------------------------------------------- 526 Method_Path: C:\\Users\\Public\\Docume... C:\\Users\\Public\\Docume... 527 Method_Name: Water Quant 1_Linear.q1 IPA Quant 1_Linear.q1 528 Date_Time_Method: 2025/04/03 12:48:16 (G... 2025/04/03 09:03:49 (G... 529 Date_Time_Analysis: 2025/04/03 21:26:09 (G... 2025/04/03 21:26:09 (G... 530 X_Startpoint: 7368.4 5874.2 531 X_Endpoint: 8127.6 5970.95 532 Component_Name: Water IPA 533 Component_Unit: % % 534 Component_Name_User: Water IPA 535 Component_Unit_User: % % 536 Formatting: %.4G %.4G 537 Prediction: 86.3654 -7.54551 538Prediction_Calculated: 86.3654 -7.54551 539 Formula: 540 Sigma: 9.65275 10.7219 541 Integration_Result: 159.336 135.308 542 Target_Concentration: 3.40282e+38 3.40282e+38 543 Warning_Upper_Limit: 3.40282e+38 3.40282e+38 544 Warning_Lower_Limit: 3.40282e+38 3.40282e+38 545 Alarm_Upper_Limit: 3.40282e+38 3.40282e+38 546 Alarm_Lower_Limit: 3.40282e+38 3.40282e+38 547 Process_Channel_Name: 548---------------------------------------------------------------------------------------------------- 549==================================================================================================== 550``` 551 552At the very top of the report, you see a centered title. This title can be accessed by the `title` 553attribute of the `Report`. 554 555```python 556report = data.reports[0] 557print(report.title) 558``` 559```console 560Multi Evaluation Test Report 561``` 562 563After the title, you see a list of report properties. These properties are stored as a `dict` in 564the `properties` attribute of a `Report`, but can also be accessed by indexing the report using the 565property key (case insensitive): 566```python 567for key, val in report.properties.items(): 568 print(key, val) 569print('\\nAccessing report properties by name:') 570print(report['Method Name'], report['Method Name'] == report['method name']) 571``` 572```console 573Version 4 574Method Path C:\\Users\\Public\\Documents\\Bruker\\OPUS_8.9.7\\ME_Base\\ME 575Method Name IPA Water Int Q1 Q2.mev 576Method Date Time 2025/04/03 17:39:01 (GMT-5) 577 578Accessing report properties by name: 579IPA Water Int Q1 Q2.mev True 580``` 581 582Following the report properties is a table. This data is stored in the `table` attribute of a 583`Report` as a `ReportTable` class (`brukeropus.file.report.ReportTable`). `ReportTable`s have 584titles, headers, and values. Below is a snippet showing how to access data from the report table: 585 586```python 587print('Table title:', report.table.title) 588print('Table Headers:', report.table.header) 589print('Table row values by name:', report.table['Type']) 590print('Table row values by index:', report.table[1]) 591print('Last value of a table row:', report.table['Type'][-1]) 592``` 593```console 594Table title: Multi Evaluation Test Report 595Table Headers: ['Type', 'Subreport', 'Row', 'Last Change'] 596Table row values by name: ['Q2', 'Q2', 'INT', 'INT', 'Q1', 'Q1'] 597Table row values by index: [1, 1, 2, 2, 3, 3] 598Last value of a table row: Q1 599``` 600 601In this report, the table is followed by a series of subreports. Because a report can have multiple 602subreports (this file has 3), they are stored as a `list` in the `sub` attribute of a `Report`. 603Subreports can be accessed by indexing the `sub` attribute, or directly indexing the `Report`. 604Because these subreports are `ReportTable`s, they have the same interface as above: 605 606```python 607print('First subreport title:', report.sub[0].title) 608print('Second subreport title:', report[1].title) 609print('First subreport Method Names:', report[0]['method_name']) 610print('First method name of the first subreport:', report[0]['method_name'][0]) 611``` 612```console 613First subreport title: Quant 2 614Second subreport title: Integration 615First subreport Method Names: ['IPA Method.q2', 'H2O Method.q2'] 616First method name of the first subreport: IPA Method.q2 617``` 618''' 619 620from brukeropus.file.block import * 621from brukeropus.file.constants import * 622from brukeropus.file.data import * 623from brukeropus.file.directory import * 624from brukeropus.file.file import * 625from brukeropus.file.labels import * 626from brukeropus.file.params import * 627from brukeropus.file.parse import * 628from brukeropus.file.report import * 629from brukeropus.file.utils import *