resistics.spectra.io module¶

class resistics.spectra.io.SpectrumReader(datapath: str)[source]¶

Bases: resistics.common.base.ResisticsBase

Reads in spectra data for measurements

Spectrum reader reads in the info file for the spectra data and .dat files (for ascii formatted spectra data) and .bin files (for binary formatted data).

Spectra files are located in: project -> specData -> site -> datapath -> spectra data files

Attributes

datapathstr: Data root for spectra data
headerKeys :: Spectra file header keys
headersDict: Spectra file header values
comments: List[str]: Spectra file comments
dataType :: Data type of spectra data
dataByteSizeint: Byte size of a single data point
filepathstr: Filepath for spectra files
filebool: The data file

Methods

__init__(datapath)	Initialise the SpectrumReader getReferenceTime() Get the reference time used for the spectrum calculation
getChannels()	Get the channels in the spectra data
getNumChannels()	Get the number of channels
getSampleFreq()	Get the sampling frequency of the data
getNumWindows()	Get the number of windows in the spectra file
getWindowSize()	Get the window size used for the data
getWindowOverlap()	Get the window overlap size
getDataSize()	Get the number of samples in a spectra window
getGlobalOffset()	Get the window global offset
getGlobalRange()	Get the window global indices range
getFrequencyArray()	Get the frequency array of the frequencies of the spectra data points
getComments()	Get a deepcopy of the comments
openBinaryForReading(filename, fileInc):	Open a binary spectra file given by filename and fileInc (the decimation level)
readBinaryWindowLocal(localIndex)	Read a spectra window given by a local index in binary format
readBinaryWindowGlobal(globalIndex)	Read a spectra window given by a global index (relative to reference time) in binary format
openAsciiForReading(filename, fileInc):	Open a ascii spectra file given by filename and fileInc (the decimation level)
readAsciiWindowLocal(localIndex)	Read a spectra window given by a local index in ascii format
readAsciiWindowGlobal(globalIndex)	Read a spectra window given by a global index (relative to reference time) in ascii format
readInfoFile(filepath)	Read the spectra information file given by filepath
getInfoValue(header, line)	Put header value in the correct format for header and line
readCommentsFile(filepath):	Read the comments file given by filepath
getFileBase(filename, fileInc):	Get the spectra file name
closeFile()	Close spectra data file
printList()	Class status returned as list of strings

closeFile(self)[source]¶: Close spectra file

getChannels(self) → List[str][source]¶

Get the channels in the spectra data

Returns

List[str]: List of channels

getComments(self) → List[str][source]¶

Get a deepcopy of the comments

Returns

List[str]: Dataset comments as a list of strings

getDataSize(self) → int[source]¶

Get the size of the corresponding spectrum data for a window

Returns

int: Number of samples in one spectrum window

getFileBase(self, filename: str, fileInc: int) → str[source]¶

Read comments file from filepath

Parameters

filename: str: Filename of spectra files
fileIncint: The decimation level

getFrequencyArray(self) → numpy.ndarray[source]¶

Returns the frequency array

Frequency array are the frequency points in the spectra

Returns

np.ndarray: Frequency array

getGlobalOffset(self) → int[source]¶

Get global window offset

The global window offset references windows to the reference time rather than the start time of the time data

Returns

int: Global window offset

getGlobalRange(self) → List[int][source]¶

Get the range of window global indices

The first global index is given by getGlobalOffset() as the counting starts from zero. The last global index is self.getGlobalOffset() + self.getNumWindows() - 1.

Returns

List[int]: List with two elements, the first being the global index of the first spectrum window and the second, the global index of the last spectrum window

getInfoValue(self, header: str, line: str) → Any[source]¶

Format some of the info file values

Parameters

headerstr: The header
linestr: The line from the info file

getNumChannels(self) → int[source]¶

Get the number of channels

Returns

int: The number of channels

getNumWindows(self) → int[source]¶

Get number of windows for which spectra have been calculated

Returns

int: The number of windows

getReferenceTime(self) → datetime.datetime[source]¶

Get reference time for spectra calculation

Returns

datetime: The reference time used for the spectra calculation

getSampleFreq(self) → float[source]¶

Get sampling frequency of time data used for spectra calculation

Returns

float: Sampling frequency of the time data

getSpectrumData(self, localIndex: int, data: Dict[str, numpy.ndarray]) → resistics.spectra.data.SpectrumData[source]¶

Return a spectrum data object from a data dictionary and the local index

Parameters

localIndexint: The local index of the spectra window
dataDict[str, np.ndarray]: The data dictionary

Returns

SpectrumData: A SpectrumData object

getWindowOverlap(self) → int[source]¶

Get the size of the time data overlap in samples

Returns

int: Size of time data overlap in samples

getWindowSize(self) → int[source]¶

Get the size of the time data window in samples

Returns

int: Size of time data window in samples

openAsciiForReading(self, filename: str, fileInc: int) → bool[source]¶

Open a ascii data file for reading

Parameters

filename: str: Filename of spectra files
fileIncint: The decimation level

openBinaryForReading(self, filename: str, fileInc: int) → bool[source]¶

Open a binary data file for reading

self.file is not set in this method because spectra data is read using memmap.

Parameters

filename: str: Filename of spectra files
fileIncint: The decimation level

printList(self) → List[str][source]¶

Class information as a list of strings

Returns

outList[str]: List of strings with information

readAsciiWindowGlobal(self, globalIndex: int) → resistics.spectra.data.SpectrumData[source]¶

Get spectrum data for a window defined by a global index (for ascii formatted data)

Parameters

globalIndex: int: The global index

readAsciiWindowLocal(self, localIndex: int) → resistics.spectra.data.SpectrumData[source]¶

Get spectrum data for a window defined by a local index (for ascii formatted data)

Parameters

localIndex: int: The local index

readBinaryBatchGlobal(self, globalIndices: Union[List[int], NoneType] = None) → Tuple[List[resistics.spectra.data.SpectrumData], numpy.ndarray][source]¶

Batch read binary windows

Batch reading binary windows allows the data for calculation to be split over multi processes

Parameters

globalIndicesList[int], None, optional: The global indices to batch read. By default, all windows will be returned if not specified

Returns

List[SpectrumData]: A list of SpectrumData objects
globalIndices: np.ndarray: An array of the global indices for the SpectrumData actually returned

readBinaryWindowGlobal(self, globalIndex: int) → resistics.spectra.data.SpectrumData[source]¶

Get spectrum data for a window defined by a global index (for binary formatted data)

Parameters

globalIndex: int: The global index

readBinaryWindowLocal(self, localIndex: int) → resistics.spectra.data.SpectrumData[source]¶

Get spectrum data for a window defined by a local index (for binary formatted data)

Parameters

localIndex: int: The local index

readCommentsFile(self, filepath: str) → None[source]¶

Read comments file from filepath

Parameters

filepathstr: Comments file path

readInfoFile(self, filepath: str) → None[source]¶

Read the info file for the spectra

Parameters

filepathstr: Info file path

class resistics.spectra.io.SpectrumWriter(datapath: str, refTime: datetime.datetime)[source]¶

Bases: resistics.common.base.ResisticsBase

Writes spectra data for measurements

Spectrum writer writes out spectra data as either binary (recommended) or ascii (more space required). A spectra file should be written out for each decimation level along with an information file, again for each decimation level. A single comments file is written out to record the processing sequence.

Spectra files are located in: project -> specData -> site -> datapath -> spectra data files

.dat files are ascii formatted data .bin files are binary formatted data

Attributes

datapathstr: Data root for spectra data
filepathstr: Filepath for spectra files
refTimedatetime: The reference time for the project
filebool: The data file

Methods

__init__(datapath, refTime)	Initialise the SpectrumWriter
openBinaryForWriting(filename, fileInc, sampleFreq, winSize, winOverlap, globalOffset, numWindows, channels)	Open file for writing binary spectra data
writeBinary(specData)	Write out binary spectra data for a single time window
openAsciiForWriting(filename, fileInc, sampleFreq, winSize, winOverlap, globalOffset, numWindows, channels)	Open file for writing ascii spectra data
writeAscii(specData)	Write out ascii spectra data for a single time window
writeInfoFile(filepath, sampleFreq, winSize, winOverlap, globalOffset, numWindows, channels)	Write out the spectra information file
writeCommentsFile(comments)	Write out the comments file
getFileBase(filename, fileInc)	Get the spectra file name
closeFile()	Close spectra data file
printList()	Class status returned as list of strings

closeFile(self)[source]¶: Close spectra file

getFileBase(self, filename: str, fileInc: int) → str[source]¶

Read comments file from filepath

Parameters

filename: str: Filename of spectra files
fileIncint: The decimation level

openAsciiForWriting(self, filename: str, fileInc: str, sampleFreq: float, winSize: int, winOverlap: int, globalOffset: int, numWindows: int, channels: List[str]) → None[source]¶

Write ascii spectrum file

Parameters

filenamestr: Filename for spectra files
fileIncint: The decimation level
sampleFreqfloat: Sampling frequeny of time data
winSizeint: Window size in samples for time data windows
winOverlapint: Overlap size in samples for time data windows
globalOffsetint: Global offset for local and global indices
numWindowsint: The number of windows in the time data
channelsList[str]: Channels in data

openBinaryForWriting(self, filename, fileInc, sampleFreq, winSize, winOverlap, globalOffset, numWindows, channels) → None[source]¶

Write binary spectrum file

Parameters

filenamestr: Filename for spectra files
fileIncint: The decimation level
sampleFreqfloat: Sampling frequeny of time data
winSizeint: Window size in samples for time data windows
winOverlapint: Overlap size in samples for time data windows
globalOffsetint: Global offset for local and global indices
numWindowsint: The number of windows in the time data
channelsList[str]: Channels in data

printList(self) → List[str][source]¶

Class information as a list of strings

Returns

outList[str]: List of strings with information

writeAscii(self, specData: resistics.spectra.data.SpectrumData) → None[source]¶

Write spectrum data to ascii file

Parameters

specDataSpectrumData: Spectrum data

writeBinary(self, specData)[source]¶

Write spectrum data to binary file

Parameters

specDataSpectrumData: Spectrum data

writeCommentsFile(self, comments: List[str]) → None[source]¶

Write comments file

Parameters

commentsList[str]: List of comments

writeInfoFile(self, filepath: str, sampleFreq: float, winSize: int, winOverlap: int, globalOffset: int, numWindows: int, channels: List[str]) → None[source]¶

Write info file

Parameters

filepathstr: Filepath for info file
sampleFreqfloat: Sampling frequeny of time data
winSizeint: Window size in samples for time data windows
winOverlapint: Overlap size in samples for time data windows
globalOffsetint: Global offset for local and global indices
numWindowsint: The number of windows in the time data
channelsList[str]: Channels in data