jpegdna.format package¶

Module contents¶

Formatter collections for the Jpeg DNA codecs

class jpegdna.format.AbstractFormatter[source]¶

Bases: abc.ABC

Abstract class for formatter definition

abstract deformat(oligos)[source]¶

Decoding method

Parameters: code (list) – Formated oligos to deformat
Returns: Deformated strand
Return type: str

abstract format(inp)[source]¶

Encoding method

Parameters: inp (str) – Strand to format
Returns: Formatted oligos
Return type: list

full_deformat(oligos, *args)[source]¶

Encoding method

Parameters

code (list) – Formated oligos to deformat
args (any) – Deformatting arguments

Returns

Deformated strand

Return type

str

full_format(inp, *args)[source]¶

Encoding method

Parameters

inp (str) – Strand to format
args (any) – Header info

Returns

Formatted oligos

Return type

list

get_state(case=None)[source]¶

Helper method to get the state of the codec if necessary

Return type: any

set_state(*args, case=None)[source]¶

Helper method to set the state of the codec if necessary

Return type: None

exception jpegdna.format.AutomataException[source]¶: Bases: Exception

exception jpegdna.format.AutomataGetterException[source]¶: Bases: jpegdna.format.AutomataException

exception jpegdna.format.AutomataGetterExceptionDeformat[source]¶: Bases: jpegdna.format.AutomataGetterException

exception jpegdna.format.AutomataGetterExceptionFormat[source]¶: Bases: jpegdna.format.AutomataGetterException

exception jpegdna.format.AutomataSetterException[source]¶: Bases: jpegdna.format.AutomataException

exception jpegdna.format.AutomataSetterExceptionDeformat[source]¶: Bases: jpegdna.format.AutomataSetterException

exception jpegdna.format.AutomataSetterExceptionFormat[source]¶: Bases: jpegdna.format.AutomataSetterException

jpegdna.format.dataformatter module¶

Formatting method for data oligo

class jpegdna.format.dataformatter.DataFormatter(header, oligo_length=200, debug=False)[source]¶

Bases: jpegdna.format.AbstractFormatter

Formatter for the strand coming out of the compression algorithm

Variables: oligo_length – Size of the oligos used for formatting

DEFAULT_OFFSET_CODE_LENGTH = 8[source]¶

deformat(oligos)[source]¶

Methods deformatting the oligos and rebuilding the data strand

Parameters: oligos (list(str)) – data oligos
Returns: data strand resulting from compression
Return type: str

format(inp)[source]¶

Method formatting the data strand into oligos

Parameters: inp (str) – strand resulting from the compression algorithm
Returns: list of formatted oligos of size self.oligo_length
Return type: list(str)

jpegdna.format.frequenciesformatter module¶

Formatting method for frequencies

class jpegdna.format.frequenciesformatter.GrayFrequenciesFormatter(max_cat, max_runcat, dc_freq_len, ac_freq_len, header, dc_header, ac_header, oligo_length=200, debug=False)[source]¶

Bases: jpegdna.format.AbstractFormatter

Formatter for the gray DC and AC frequencies

Variables

max_cat – max value for the categories
max_runcat – max value for the run/categories
dc_freq_len – codeword length for encoding the dc frequencies
ac_freq_len – codeword length for encoding the ac frequencies
oligo_length – Size of the oligos used for formatting

DEFAULT_FREQUENCIES_OFFSET_CODE_LENGTH = 7[source]¶

decode_frequencies(strand, freq_type)[source]¶

Decode the frequencies using fixed-length codebooks

Parameters

strand (str) – encoded frequency values
freq_type (str) – DC/AC frequency indicator

Returns

list of frequency values

Return type

list(int)

deformat(oligos)[source]¶

Deformats and decodes both DC and AC frequency oligos

Parameters: oligos (list(str)) – formatted frequency oligos for AC and DC
Returns: decoded frequency tables
Return type: tuple(list(int))

deformat_frequencies(oligos)[source]¶

Deformat the oligos describing either the DC or the AC frequencies

Parameters

oligos – oligos to deformat
freq_type (str) – DC/AC frequency indicator

Returns

strand encoding the frequencies

Return type

str

encode_frequencies(freqs, freq_type)[source]¶

Encode the frequencies using fixed-length codebooks

Parameters

freqs (list(int)) – frequency values to encode
freq_type (str) – DC/AC frequency indicator

Returns

strand encoding the frequencies

Return type

str

format(inp)[source]¶

Encodes and formats both DC and AC frequencies

Parameters: inp (tuple(list(int))) – frequencies for DC categories and AC run/categories
Returns: formatted frequency oligos
Return type: list(str)

format_frequencies(inp, freq_type)[source]¶

Format the strand encoding either the DC or the AC frequencies

Parameters

inp (str) – strand to format
freq_type (str) – DC/AC frequency indicator

Returns

formatted AC or DC frequency oligos

Return type

list(str)

class jpegdna.format.frequenciesformatter.RGBFrequenciesFormatter(max_cat, max_runcat, dc_freq_len, ac_freq_len, header, dc_header, ac_header, oligo_length=200, debug=False)[source]¶

Bases: jpegdna.format.frequenciesformatter.GrayFrequenciesFormatter

Formatter for the RGB DC and AC frequencies

Variables

max_cat – max value for the categories
max_runcat – max value for the run/categories
dc_freq_len – codeword length for encoding the dc frequencies
ac_freq_len – codeword length for encoding the ac frequencies
oligo_length – Size of the oligos used for formatting

deformat(oligos)[source]¶

Deformats and decodes both DC and AC frequency oligos

Parameters: oligos (list(str)) – formatted frequency oligos for AC and DC
Returns: decoded frequency tables
Return type: tuple(tuple(list(int)))

format(inp)[source]¶

Encodes and formats both DC and AC frequencies

Parameters: inp (tuple(tuple(list(int)))) – frequencies for DC categories and AC run/categories
Returns: formatted frequency oligos
Return type: list(str)

jpegdna.format.generalinfoformatter module¶

Formatting method for general info oligo

class jpegdna.format.generalinfoformatter.GeneralInfoFormatter(alpha, freq_origin, m, n, blockdims, max_cat, max_runcat, dc_freq_len, ac_freq_len, image_type, sampler, header, oligo_length=200, debug=False)[source]¶

Bases: jpegdna.format.AbstractFormatter

Formatter for the general information related to the compression

Variables

alpha – alpha value of the compression, if it is known
freq_origin – origin of the frequencies (“default” or “from_img”)
m – first dimension of the image
n – second dimension of the image
blockdims – dimensions of the block used for DCT
max_cat – max value for the categories
max_runcat – max value for the run/categories
dc_freq_len – codeword length for encoding the dc frequencies
ac_freq_len – codeword length for encoding the ac frequencies
oligo_length – Size of the oligos used for formatting

IMAGE_TYPES = ['gray', 'RGB'][source]¶

colored_image()[source]¶

Check if image is colored or gray level

Return type: bool

deformat(oligos)[source]¶

Decoding method

Parameters: code (list) – Formated oligos to deformat
Returns: Deformated strand
Return type: str

format(inp)[source]¶

Encoding method

Parameters: inp (str) – Strand to format
Returns: Formatted oligos
Return type: list

jpegdna.format.jpegdnaformatter module¶

Gray-level strand formatter

class jpegdna.format.jpegdnaformatter.JpegDNAFormatter(alpha, image_type, sampler='4:2:2', freq_origin=None, primer='illumina', oligo_length=200, debug=False)[source]¶

Bases: jpegdna.format.AbstractFormatter

Jpeg DNA gray level formatter class

Parameters

aplha – Alpha value (quantization step multiplier)
freq_origin (str) – Choose between default and adapted frequencies
primer (str) – Primer name used

DEFAULT_AC_FREQ_HEADER = 'AGAG'[source]¶

DEFAULT_AC_FREQ_LEN = 10[source]¶

DEFAULT_BLOCKDIMS = (8, 8)[source]¶

DEFAULT_CENTERING_OFFSET = 75[source]¶

DEFAULT_DATA_INFO_HEADER = 'TTGAGGA'[source]¶

DEFAULT_DC_FREQ_HEADER = 'ATTC'[source]¶

DEFAULT_DC_FRQ_LEN = 7[source]¶

DEFAULT_FREQS_INFO_HEADER = 'ATCCGTC'[source]¶

DEFAULT_GENERAL_INFO_HEADER = 'AATAATA'[source]¶

DEFAULT_MAX_CAT = 11[source]¶

DEFAULT_MAX_RUNCAT = 162[source]¶

PRIMERS = {'illumina': ('GTTCAGAGTTCTACAGTCCGACGATC', 'TGGAATTCTCGGGTGCCAAGG'), 'none': ('', '')}[source]¶

PRIMER_LENGTHS = {'illumina': (26, 21), 'none': (0, 0)}[source]¶

add_ids(oligos, n)[source]¶

Adding primers to formatted oligos

Parameters: oligos (list) – list of formatted oligos without offset
Returns: list of oligos with offset added at the beginning of each oligo
Rtpye: list

add_parity_strand(data, image_id, sense_nt)[source]¶

Computes the parity strand for the current oligo

Parameters

data (str) – strand on which to compute parities for each base
image_id (str) – id of the image
sense_nt – sense nucelotide

add_primers_and_sense(oligos)[source]¶

Adding primers to formatted oligos

Parameters: oligos (list) – list of formatted oligos without primers
Returns: list of oligos with primers added at the beginning and at the end of each oligo
Rtpye: list

add_sense_nt(pos)[source]¶

Compute the sens nucleotide either the beginning one or the ending one

Parameters: pos (str) – either “begin” or “end”, position of the sense nt to compute
Returns: sense nucleotide
Return type: str

cut_payload(el, n)[source]¶

Cuts the payoad in two halves after the n-th nucleotide

Parameters: el (string) – Stand to be cut
Returns: Two cuts
Return type: Tuple(string)

deformat(oligos)[source]¶

Decoding method

Parameters: code (list) – Formated oligos to deformat
Returns: Deformated strand
Return type: str

format(inp)[source]¶

Encoding method

Parameters: inp (str) – Strand to format
Returns: Formatted oligos
Return type: list

full_deformat(oligos, *args)[source]¶

Encoding method

Parameters

code (list) – Formated oligos to deformat
args (any) – Deformatting arguments

Returns

Deformated strand

Return type

str

full_format(inp, *args)[source]¶

Encoding method

Parameters

inp (str) – Strand to format
args (any) – Header info

Returns

Formatted oligos

Return type

list

get_payload(oligos)[source]¶

Taking primers and sense nts off formatted oligos

Parameters: oligos (list) – list of formatted oligos without primers
Returns: list of oligos with primers added at the beginning and at the end of each oligo
Rtpye: list

get_state(case=None)[source]¶: Helper method to get the state of the codec if necessary

set_alpha(alpha)[source]¶: Set alpha value

set_freq_origin(choice)[source]¶: Set frequency origin

set_primer()[source]¶: Sets the primer from the primer type

set_state(*args, case=None)[source]¶: Helper method to set the state of the codec if necessary