diff --git a/.buildinfo b/.buildinfo new file mode 100644 index 00000000..b637720f --- /dev/null +++ b/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: a0fcf460302088f3b558fee9146ad410 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/.doctrees/_autosummary/acq2sqlite.doctree b/.doctrees/_autosummary/acq2sqlite.doctree new file mode 100644 index 00000000..c3bd41b7 Binary files /dev/null and b/.doctrees/_autosummary/acq2sqlite.doctree differ diff --git a/.doctrees/_autosummary/change_header.doctree b/.doctrees/_autosummary/change_header.doctree new file mode 100644 index 00000000..e41c0cea Binary files /dev/null and b/.doctrees/_autosummary/change_header.doctree differ diff --git a/.doctrees/_autosummary/dcmmeta2tsv.doctree b/.doctrees/_autosummary/dcmmeta2tsv.doctree new file mode 100644 index 00000000..40406a1c Binary files /dev/null and b/.doctrees/_autosummary/dcmmeta2tsv.doctree differ diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle new file mode 100644 index 00000000..86803b35 Binary files /dev/null and b/.doctrees/environment.pickle differ diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree new file mode 100644 index 00000000..1173ac5e Binary files /dev/null and b/.doctrees/index.doctree differ diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 00000000..e69de29b diff --git a/_autosummary/acq2sqlite.html b/_autosummary/acq2sqlite.html new file mode 100644 index 00000000..2efe5359 --- /dev/null +++ b/_autosummary/acq2sqlite.html @@ -0,0 +1,318 @@ + + + + + + + + acq2sqlite — mrrc-hdr-qa documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

acq2sqlite

+

Convert db.txt into a sqlite database.

+

Functions

+ + + + + + + + + +

column_names()

These names match what's used by dcmmeta2tsv.py and 00_build_db.bash CSA first, normal dicom headers, and then filename.

have_pipe_data()

+

Classes

+ + + + + + +

DBQuery([sql])

Convenient SQL queries for tracking dicom headers/metadata.

+
+
+class acq2sqlite.DBQuery(sql=None)[source]
+

Convenient SQL queries for tracking dicom headers/metadata.

+

This class is a poorly implemented, ad-hoc/bespoke ORM for database defined in schema.sql

+
+
+CONSTS = ['Project', 'SequenceName', 'iPAT', 'Comments', 'SequenceType', 'PED_major', 'Phase', 'TR', 'TE', 'Matrix', 'PixelResol', 'BWP', 'BWPPE', 'FA', 'TA', 'FoV'][source]
+

CONSTS is a list of expected aquisition-invarient parameters. +The values of these attributes should be the same for every acquisition +sharing a Project × SequenceName pair (across all sessions of a Project).

+

We consider the acquisition to have a Quallity Assurance error +when the value of any of these parameters in a single acquisition +fails to match the template.

+

For example TR for task EPI acquisition identified by +SequenceName=RewardedAnti in Project=WPC-8620 +should always be 1300 ms.

+../_images/nonconforming_example.png +
+ +
+
+check_acq(d)[source]
+

Is this exact acquisition (time, id, series) already in the database?

+
+
Parameters:
+

d (dict[str, str]) – All parameters of an acquisition

+
+
Returns:
+

True/False if dict params exist

+
+
Return type:
+

bool

+
+
+
+ +
+
+dict_to_db_row(d)[source]
+

insert a dicom header (representative of acquisition) into db

+
+
Parameters:
+

d (dict[str, str])

+
+
Return type:
+

None

+
+
+
+ +
+
+get_template(pname, seqname)[source]
+

Find the template from template_by_count. See make_template_by_count.sql

+
+
Parameters:
+
    +

  • pname (str) – protocol name

    • +

  • sqname – sequence name

    • +

  • seqname (str)

    • +
+
+
Returns:
+

template row matching prot+seq name pair

+
+
Return type:
+

Row

+
+
+
+ +
+
+is_template(param_id)[source]
+

Check if param id is the ideal template.

+
+
Parameters:
+

param_id (int)

+
+
Return type:
+

bool

+
+
+
+ +
+
+param_rowid(d)[source]
+
+
Parameters:
+

d (dict[str, str]) – dicom headers

+
+
Returns:
+

acq_param (new or existing) rowid identifying unique set of CONSTS

+
+
Return type:
+

int | None

+
+
+

Find or insert the combination of parameters for an acquisition. +Using CONSTS, the header parameters that should be invariant +across acquisitions of the same name within a study.

+
>>> db = DBQuery(sqlite3.connect(':memory:'))
+>>> with open('schema.sql') as f: _ = [db.sql.execute(c) for c in f.read().split(";")]
+...
+>>> # db.sql.execute(".read schema.sql")
+>>> example = {k: 'x' for k in db.CONSTS}
+>>> db.param_rowid(example)
+1
+>>> db.param_rowid(example)
+1
+>>> db.param_rowid({**example, 'Project': 'b'})
+2
+>>> str(db.param_rowid({}))
+'None'
+
+
+
+ +
+
+search_acq_param(d)[source]
+

Try to find aca_param row id of CONSTS part of input d

+
+
Parameters:
+

d (dict[str, str]) – dictionary of tag values (keys in CONSTS)

+
+
Returns:
+

rowid of matching (param_id) or None

+
+
Return type:
+

int | None

+
+
+
+ +
+
+tsv_to_dict(line)[source]
+

Read a tsv line into dictionary.

+
+
Parameters:
+

line (str) – tab separated string. likely line from dcmmeta2tsv.py

+
+
Returns:
+

dictionary with taglist.txt names and acquisition values.

+
+
Return type:
+

dict[str, str]

+
+
+
+ +
+ +
+
+acq2sqlite.column_names()[source]
+

These names match what’s used by dcmmeta2tsv.py and 00_build_db.bash +CSA first, normal dicom headers, and then filename.

+

Defaults to reading from taglist.txt +This provides a language agnostic lookup for columns in schema.sql

+

These column names should match what is output by +./dcmmeta2tsv.bash or ./dcmmeta2tsv.py

+

Also see dcmmeta2tsv.read_known_tags()

+
>>> cn = column_names() # reads taglist.txt
+>>> cn[0] # hard coded here
+'Phase'
+>>> cn[3] # from taglist.xt
+'AcqDate'
+
+
+
+ +
+ + +
+ +
+
+ +
+
+
+ ©2024, EH, WF. + + | + Powered by Sphinx 8.1.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/_autosummary/change_header.html b/_autosummary/change_header.html new file mode 100644 index 00000000..21664a4f --- /dev/null +++ b/_autosummary/change_header.html @@ -0,0 +1,254 @@ + + + + + + + + change_header — mrrc-hdr-qa documentation + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

change_header

+

Modify DICOM header information to simulate failing QA.

+

Functions

+ + + + + + + + + + + + + + + + + + +

change_tags(dcm_dir, new_data[, out_dir])

Change specified tags of all dicoms in a directory.

gen_acqdates()

Generate DataElements for random acquisition day and time.

gen_anon()

Make random date of birth, age, and sex.

gen_ids(new_id)

Generate ID DataElements.

main_make_mods()

Exercise header modification code to make example data we can use.

+
+
+change_header.change_tags(dcm_dir, new_data, out_dir=None)[source]
+

Change specified tags of all dicoms in a directory. Optionally make copies in out_dir.

+

sideffect: writes copies of dcm_dir dicoms into out_dir unless out_dir is None.

+
+
Parameters:
+
    +

  • dcm_dir (Path) – input directory with dicom files (MR*, *IMA , or *dcm)

    • +

  • new_data (List[DataElement]) – list of data elements to replace +like [pydicom.DataElement(value="newpname", VR="LO", tag=(0x0018, 0x1030))]

    • +

  • out_dir (Path | None) – Optional. Where to save modified dicoms

    • +
+
+
Returns:
+

example modified dicom. last if out_dir, first and only if no out_dir.

+
+
Return type:
+

FileDataset | None

+
+
+
>>> new_data = [pydicom.DataElement(value="newpname", VR="LO", tag=(0x0018, 0x1030))]
+>>> ex_path = Path('example_dicoms/')
+>>> ex = change_tags(ex_path, new_data)
+>>> ex.ProtocolName
+'newpname'
+
+
+
+ +
+
+change_header.gen_acqdates()[source]
+

Generate DataElements for random acquisition day and time.

+
+
Returns:
+

ID DataElements List

+
+
Return type:
+

List[DataElement]

+
+
+

See gen_anon() for tag and VR info.

+
+ +
+
+change_header.gen_anon()[source]
+

Make random date of birth, age, and sex.

+
+
Returns:
+

list of DataElements with randomized values

+
+
Return type:
+

List[DataElement]

+
+
+
+

Tip

+

Field tag type and location can be extracted like:

+
x = pydicom.dcmread(example_fname)
+fields = ['AcquisitionDate', 'AcquisitionTime',
+          'PatientBirthDate', 'PatientAge', 'PatientSex']
+[x[k] for k in fields]
+
+# yields
+[(0008,0022) Acquisition Date                    DA: '20221222',
+ (0008,0032) Acquisition Time                    TM: '092132.722500',
+ (0010,0030) Patient's Birth Date                DA: '20070404',
+ (0010,1010) Patient's Age                       AS: '015Y',
+ (0010,0040) Patient's Sex                       CS: 'F']
+
+
+
+

Where the tag is the tuple and “XX:” is the type

+
+ +
+
+change_header.gen_ids(new_id)[source]
+

Generate ID DataElements.

+
+
Parameters:
+

new_id (str) – id string to put into pat name and pat id dicom headers.

+
+
Returns:
+

ID DataElements List

+
+
Return type:
+

List[DataElement]

+
+
+

See gen_anon() for tag and VR info.

+
>>> data_els = gen_ids('example_name')
+>>> data_els[0].value
+'example_name'
+>>> data_els[0].VR
+'PN'
+>>> data_els[0].tag
+(0010,0010)
+
+
+
+ +
+
+change_header.main_make_mods()[source]
+

Exercise header modification code to make example data we can use.

+

We can confirm changes are made from shell using AFNI’s dicom_hinfo

+
find example/dicom/mod* -iname 'MR*' -exec dicom_hinfo -tag 0010,0010 -sepstr $'\t' -last {} \+
+
+#   mod1 example/dicom/mod1/HabitTask/MR.1.3.12.2.1107.5.2.43.167046.2022122209214150118864465
+#   mod1 example/dicom/mod1/HabitTask/MR.1.3.12.2.1107.5.2.43.167046.2022122209214176799264617
+#   mod2 example/dicom/mod2/HabitTask/MR.1.3.12.2.1107.5.2.43.167046.2022122209214150118864465
+#   mod2 example/dicom/mod2/HabitTask/MR.1.3.12.2.1107.5.2.43.167046.2022122209214176799264617
+
+
+
+ +
+ + +
+ +
+
+ +
+
+
+ ©2024, EH, WF. + + | + Powered by Sphinx 8.1.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/_autosummary/dcmmeta2tsv.html b/_autosummary/dcmmeta2tsv.html new file mode 100644 index 00000000..9a7fd652 --- /dev/null +++ b/_autosummary/dcmmeta2tsv.html @@ -0,0 +1,320 @@ + + + + + + + + dcmmeta2tsv — mrrc-hdr-qa documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

dcmmeta2tsv

+

Give a tab separated metadata value line per dicom file.

+

Module Attributes

+ + + + + + + + + +

NULLVAL

object that has obj.value for when a dicom tag does not exist using 'null' to match AFNI's dicom_hinfo

TagValues

keys are names from taglist.txt, also has dcm_path key for file

+

Functions

+ + + + + + + + + + + + + + + + + + +

csa_fetch(csa_tr, itemname)

safely look into csa_tr dicom dictionary.

read_csa(csa)

extract parameters from siemens CSA :param csa: content of siemens private tag (0x0029, 0x1010) :return: [pepd, ipat] is phase encode positive direction and GRAPA iPATModeText

read_known_tags([tagfile])

read in tsv file like with header name,tag,desc.

read_tags(dcm_path, tags)

Read dicom header and isolate tags

tagpair_to_hex(csv_str)

move our text files has tags like "0051,1017" to pydicom indexe like (0x51,0x1017)

+

Classes

+ + + + + + +

DicomTagReader()

Class to cache read_known_tags() output

+
+
+class dcmmeta2tsv.DicomTagReader[source]
+

Class to cache read_known_tags() output

+
+
+read_dicom_tags(dcm_path)[source]
+

return values of dicom header priority fields +ordered as defined in taglist.txt +:param dcm_path: path to dciom +:return: dict[taglist.txt tagname, tag value]

+
>>> dtr = DicomTagReader()
+>>> hdr = dtr.read_dicom_tags('example_dicoms/RewardedAnti_good.dcm')
+>>> list(hdr.values()) 
+[1, 'p2', '154833.265000', '20220913', ...
+
+
+
>>> list(hdr.values())[-1]
+'example_dicoms/RewardedAnti_good.dcm'
+
+
+
+
Parameters:
+

dcm_path (PathLike)

+
+
Return type:
+

dict[str, str]

+
+
+
+ +
+ +
+
+dcmmeta2tsv.NULLVAL = <dcmmeta2tsv. object>[source]
+

object that has obj.value for when a dicom tag does not exist +using ‘null’ to match AFNI’s dicom_hinfo

+
+ +
+
+dcmmeta2tsv.TagValues[source]
+

keys are names from taglist.txt, also has dcm_path key for file

+
+ +
+
+dcmmeta2tsv.csa_fetch(csa_tr, itemname)[source]
+

safely look into csa_tr dicom dictionary. +Expect nested structure like 'tags'->itemname->'items'->[0].

+

In future, might want to check itemname and pull out more than the first array item.

+
>>> csa_fetch({'notags':'badinput'}, 'PhaseEncodingDirectionPositive')
+'null'
+>>> csa_fetch({'tags':{'ImaPATModeText': {'items': [1]}}}, 'ImaPATModeText')
+1
+
+
+
+
Parameters:
+
    +

  • csa_tr (dict)

    • +

  • itemname (str)

    • +
+
+
Return type:
+

str

+
+
+
+ +
+
+dcmmeta2tsv.read_csa(csa)[source]
+

extract parameters from siemens CSA +:param csa: content of siemens private tag (0x0029, 0x1010) +:return: [pepd, ipat] is phase encode positive direction and GRAPA iPATModeText

+
>>> read_csa(None) is None
+True
+
+
+
+
Return type:
+

list[str]

+
+
+
+ +
+
+dcmmeta2tsv.read_known_tags(tagfile='taglist.txt')[source]
+

read in tsv file like with header name,tag,desc. +skip comments and header

+
+
Parameters:
+

tagfile – text tsv file to get name,tag(hex pair),desc from

+
+
Returns:
+

file parsed into a list of dictonaires

+
+
Return type:
+

list[Tag]

+
+
+
+ +
+
+dcmmeta2tsv.read_tags(dcm_path, tags)[source]
+

Read dicom header and isolate tags

+
+
Parameters:
+
    +

  • dcm_path (PathLike) – dicom file with headers to extract

    • +

  • tags (list[Tag]) – ordered dictionary with ‘tag’ key as hex pair, see tagpair_to_hex()

    • +
+
+
Returns:
+

dict[tag,value] values in same order as tags

+
+
Return type:
+

dict[str, str]

+
+
+
>>> tr = {'name': 'TR', 'tag': (0x0018,0x0080), 'loc': 'header'}
+>>> ipat = {'name': 'iPAT', 'tag': 'ImaPATModeText', 'loc': 'csa'}
+>>> list(read_tags('example_dicoms/RewardedAnti_good.dcm', [ipat, tr]).values())
+['p2', '1300', 'example_dicoms/RewardedAnti_good.dcm']
+
+
+
>>> list(read_tags('example_dicoms/DNE.dcm', [ipat,tr]).values())
+['null', 'null', 'example_dicoms/DNE.dcm']
+
+
+
+ +
+
+dcmmeta2tsv.tagpair_to_hex(csv_str)[source]
+

move our text files has tags like “0051,1017” +to pydicom indexe like (0x51,0x1017)

+
+
Parameters:
+

csv_str – comma separated string to convert

+
+
Returns:
+

dicom header tag hex pair

+
+
Return type:
+

tuple[int, int]

+
+
+
>>> tagpair_to_hex("0051,1017")
+('0x51', '0x1017')
+
+
+
+ +
+ + +
+ +
+
+ +
+
+
+ ©2024, EH, WF. + + | + Powered by Sphinx 8.1.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/_images/nonconforming_example.png b/_images/nonconforming_example.png new file mode 100644 index 00000000..a7ccaed0 Binary files /dev/null and b/_images/nonconforming_example.png differ diff --git a/_sources/_autosummary/acq2sqlite.rst.txt b/_sources/_autosummary/acq2sqlite.rst.txt new file mode 100644 index 00000000..60989005 --- /dev/null +++ b/_sources/_autosummary/acq2sqlite.rst.txt @@ -0,0 +1,19 @@ +acq2sqlite +========== + +.. automodule:: acq2sqlite + + + .. rubric:: Functions + + .. autosummary:: + + column_names + have_pipe_data + + .. rubric:: Classes + + .. autosummary:: + + DBQuery + \ No newline at end of file diff --git a/_sources/_autosummary/change_header.rst.txt b/_sources/_autosummary/change_header.rst.txt new file mode 100644 index 00000000..259c2f08 --- /dev/null +++ b/_sources/_autosummary/change_header.rst.txt @@ -0,0 +1,16 @@ +change\_header +============== + +.. automodule:: change_header + + + .. rubric:: Functions + + .. autosummary:: + + change_tags + gen_acqdates + gen_anon + gen_ids + main_make_mods + \ No newline at end of file diff --git a/_sources/_autosummary/dcmmeta2tsv.rst.txt b/_sources/_autosummary/dcmmeta2tsv.rst.txt new file mode 100644 index 00000000..46424eaf --- /dev/null +++ b/_sources/_autosummary/dcmmeta2tsv.rst.txt @@ -0,0 +1,29 @@ +dcmmeta2tsv +=========== + +.. automodule:: dcmmeta2tsv + + + .. rubric:: Module Attributes + + .. autosummary:: + + NULLVAL + TagValues + + .. rubric:: Functions + + .. autosummary:: + + csa_fetch + read_csa + read_known_tags + read_tags + tagpair_to_hex + + .. rubric:: Classes + + .. autosummary:: + + DicomTagReader + \ No newline at end of file diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 00000000..eb645d4d --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,52 @@ +.. mrrc-hdr-qa documentation master file, created by + sphinx-quickstart on Mon Oct 21 19:00:25 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +mrrc-hdr-qa documentation +========================= + +Code to parse dicoms into a template database and alert on non-conforming sequences. + +Code +-------- + +.. toctree:: + :caption: Contents: + +.. autosummary:: + :toctree: _autosummary + :recursive: + + mrqart + dcmmeta2tsv + acq2sqlite + change_header + + +Overview +-------- + + +Template +++++++++ + +See :py:data:`acq2sqlite.DBQuery.CONSTS` + +Here's an example for the ``RewardedAnti`` task acquisitions in the ``WPC-8620`` project. The ideal template is found finding the most frequent set of repeated key parameters. 150 of the ``RewardedAnti`` seqeuences share the same ``acq_param`` set, here stored in the sqlite db on rowid=35. But 4 acquisitions (rows in ``acq``) don't match. In this case all mismatches can be found in ``TA``. + +.. image:: ../sphinx/imgs/nonconforming_example.png + + + +.. `https://dicom-parser.readthedocs.io/en/latest/siemens/csa_headers.html#csa-headers`_ + + +Parameters +---------- + + .. csv-table:: Dicom tag list + :file: ../docs/taglist.csv + :header-rows: 1 + +.. .. include:: ../readme.md diff --git a/_static/alabaster.css b/_static/alabaster.css new file mode 100644 index 00000000..7e75bf8f --- /dev/null +++ b/_static/alabaster.css @@ -0,0 +1,663 @@ +/* -- page layout ----------------------------------------------------------- */ + +body { + font-family: Georgia, serif; + font-size: 17px; + background-color: #fff; + color: #000; + margin: 0; + padding: 0; +} + + +div.document { + width: 940px; + margin: 30px auto 0 auto; +} + +div.documentwrapper { + float: left; + width: 100%; +} + +div.bodywrapper { + margin: 0 0 0 220px; +} + +div.sphinxsidebar { + width: 220px; + font-size: 14px; + line-height: 1.5; +} + +hr { + border: 1px solid #B1B4B6; +} + +div.body { + background-color: #fff; + color: #3E4349; + padding: 0 30px 0 30px; +} + +div.body > .section { + text-align: left; +} + +div.footer { + width: 940px; + margin: 20px auto 30px auto; + font-size: 14px; + color: #888; + text-align: right; +} + +div.footer a { + color: #888; +} + +p.caption { + font-family: inherit; + font-size: inherit; +} + + +div.relations { + display: none; +} + + +div.sphinxsidebar { + max-height: 100%; + overflow-y: auto; +} + +div.sphinxsidebar a { + color: #444; + text-decoration: none; + border-bottom: 1px dotted #999; +} + +div.sphinxsidebar a:hover { + border-bottom: 1px solid #999; +} + +div.sphinxsidebarwrapper { + padding: 18px 10px; +} + +div.sphinxsidebarwrapper p.logo { + padding: 0; + margin: -10px 0 0 0px; + text-align: center; +} + +div.sphinxsidebarwrapper h1.logo { + margin-top: -10px; + text-align: center; + margin-bottom: 5px; + text-align: left; +} + +div.sphinxsidebarwrapper h1.logo-name { + margin-top: 0px; +} + +div.sphinxsidebarwrapper p.blurb { + margin-top: 0; + font-style: normal; +} + +div.sphinxsidebar h3, +div.sphinxsidebar h4 { + font-family: Georgia, serif; + color: #444; + font-size: 24px; + font-weight: normal; + margin: 0 0 5px 0; + padding: 0; +} + +div.sphinxsidebar h4 { + font-size: 20px; +} + +div.sphinxsidebar h3 a { + color: #444; +} + +div.sphinxsidebar p.logo a, +div.sphinxsidebar h3 a, +div.sphinxsidebar p.logo a:hover, +div.sphinxsidebar h3 a:hover { + border: none; +} + +div.sphinxsidebar p { + color: #555; + margin: 10px 0; +} + +div.sphinxsidebar ul { + margin: 10px 0; + padding: 0; + color: #000; +} + +div.sphinxsidebar ul li.toctree-l1 > a { + font-size: 120%; +} + +div.sphinxsidebar ul li.toctree-l2 > a { + font-size: 110%; +} + +div.sphinxsidebar input { + border: 1px solid #CCC; + font-family: Georgia, serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox { + margin: 1em 0; +} + +div.sphinxsidebar .search > div { + display: table-cell; +} + +div.sphinxsidebar hr { + border: none; + height: 1px; + color: #AAA; + background: #AAA; + + text-align: left; + margin-left: 0; + width: 50%; +} + +div.sphinxsidebar .badge { + border-bottom: none; +} + +div.sphinxsidebar .badge:hover { + border-bottom: none; +} + +/* To address an issue with donation coming after search */ +div.sphinxsidebar h3.donation { + margin-top: 10px; +} + +/* -- body styles ----------------------------------------------------------- */ + +a { + color: #004B6B; + text-decoration: underline; +} + +a:hover { + color: #6D4100; + text-decoration: underline; +} + +div.body h1, +div.body h2, +div.body h3, +div.body h4, +div.body h5, +div.body h6 { + font-family: Georgia, serif; + font-weight: normal; + margin: 30px 0px 10px 0px; + padding: 0; +} + +div.body h1 { margin-top: 0; padding-top: 0; font-size: 240%; } +div.body h2 { font-size: 180%; } +div.body h3 { font-size: 150%; } +div.body h4 { font-size: 130%; } +div.body h5 { font-size: 100%; } +div.body h6 { font-size: 100%; } + +a.headerlink { + color: #DDD; + padding: 0 4px; + text-decoration: none; +} + +a.headerlink:hover { + color: #444; + background: #EAEAEA; +} + +div.body p, div.body dd, div.body li { + line-height: 1.4em; +} + +div.admonition { + margin: 20px 0px; + padding: 10px 30px; + background-color: #EEE; + border: 1px solid #CCC; +} + +div.admonition tt.xref, div.admonition code.xref, div.admonition a tt { + background-color: #FBFBFB; + border-bottom: 1px solid #fafafa; +} + +div.admonition p.admonition-title { + font-family: Georgia, serif; + font-weight: normal; + font-size: 24px; + margin: 0 0 10px 0; + padding: 0; + line-height: 1; +} + +div.admonition p.last { + margin-bottom: 0; +} + +dt:target, .highlight { + background: #FAF3E8; +} + +div.warning { + background-color: #FCC; + border: 1px solid #FAA; +} + +div.danger { + background-color: #FCC; + border: 1px solid #FAA; + -moz-box-shadow: 2px 2px 4px #D52C2C; + -webkit-box-shadow: 2px 2px 4px #D52C2C; + box-shadow: 2px 2px 4px #D52C2C; +} + +div.error { + background-color: #FCC; + border: 1px solid #FAA; + -moz-box-shadow: 2px 2px 4px #D52C2C; + -webkit-box-shadow: 2px 2px 4px #D52C2C; + box-shadow: 2px 2px 4px #D52C2C; +} + +div.caution { + background-color: #FCC; + border: 1px solid #FAA; +} + +div.attention { + background-color: #FCC; + border: 1px solid #FAA; +} + +div.important { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.note { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.tip { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.hint { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.seealso { + background-color: #EEE; + border: 1px solid #CCC; +} + +div.topic { + background-color: #EEE; +} + +p.admonition-title { + display: inline; +} + +p.admonition-title:after { + content: ":"; +} + +pre, tt, code { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; + font-size: 0.9em; +} + +.hll { + background-color: #FFC; + margin: 0 -12px; + padding: 0 12px; + display: block; +} + +img.screenshot { +} + +tt.descname, tt.descclassname, code.descname, code.descclassname { + font-size: 0.95em; +} + +tt.descname, code.descname { + padding-right: 0.08em; +} + +img.screenshot { + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils { + border: 1px solid #888; + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils td, table.docutils th { + border: 1px solid #888; + padding: 0.25em 0.7em; +} + +table.field-list, table.footnote { + border: none; + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + +table.footnote { + margin: 15px 0; + width: 100%; + border: 1px solid #EEE; + background: #FDFDFD; + font-size: 0.9em; +} + +table.footnote + table.footnote { + margin-top: -15px; + border-top: none; +} + +table.field-list th { + padding: 0 0.8em 0 0; +} + +table.field-list td { + padding: 0; +} + +table.field-list p { + margin-bottom: 0.8em; +} + +/* Cloned from + * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68 + */ +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +table.footnote td.label { + width: .1px; + padding: 0.3em 0 0.3em 0.5em; +} + +table.footnote td { + padding: 0.3em 0.5em; +} + +dl { + margin-left: 0; + margin-right: 0; + margin-top: 0; + padding: 0; +} + +dl dd { + margin-left: 30px; +} + +blockquote { + margin: 0 0 0 30px; + padding: 0; +} + +ul, ol { + /* Matches the 30px from the narrow-screen "li > ul" selector below */ + margin: 10px 0 10px 30px; + padding: 0; +} + +pre { + background: unset; + padding: 7px 30px; + margin: 15px 0px; + line-height: 1.3em; +} + +div.viewcode-block:target { + background: #ffd; +} + +dl pre, blockquote pre, li pre { + margin-left: 0; + padding-left: 30px; +} + +tt, code { + background-color: #ecf0f3; + color: #222; + /* padding: 1px 2px; */ +} + +tt.xref, code.xref, a tt { + background-color: #FBFBFB; + border-bottom: 1px solid #fff; +} + +a.reference { + text-decoration: none; + border-bottom: 1px dotted #004B6B; +} + +a.reference:hover { + border-bottom: 1px solid #6D4100; +} + +/* Don't put an underline on images */ +a.image-reference, a.image-reference:hover { + border-bottom: none; +} + +a.footnote-reference { + text-decoration: none; + font-size: 0.7em; + vertical-align: top; + border-bottom: 1px dotted #004B6B; +} + +a.footnote-reference:hover { + border-bottom: 1px solid #6D4100; +} + +a:hover tt, a:hover code { + background: #EEE; +} + +@media screen and (max-width: 940px) { + + body { + margin: 0; + padding: 20px 30px; + } + + div.documentwrapper { + float: none; + background: #fff; + margin-left: 0; + margin-top: 0; + margin-right: 0; + margin-bottom: 0; + } + + div.sphinxsidebar { + display: block; + float: none; + width: unset; + margin: 50px -30px -20px -30px; + padding: 10px 20px; + background: #333; + color: #FFF; + } + + div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p, + div.sphinxsidebar h3 a { + color: #fff; + } + + div.sphinxsidebar a { + color: #AAA; + } + + div.sphinxsidebar p.logo { + display: none; + } + + div.document { + width: 100%; + margin: 0; + } + + div.footer { + display: none; + } + + div.bodywrapper { + margin: 0; + } + + div.body { + min-height: 0; + min-width: auto; /* fixes width on small screens, breaks .hll */ + padding: 0; + } + + .hll { + /* "fixes" the breakage */ + width: max-content; + } + + .rtd_doc_footer { + display: none; + } + + .document { + width: auto; + } + + .footer { + width: auto; + } + + .github { + display: none; + } + + ul { + margin-left: 0; + } + + li > ul { + /* Matches the 30px from the "ul, ol" selector above */ + margin-left: 30px; + } +} + + +/* misc. */ + +.revsys-inline { + display: none!important; +} + +/* Hide ugly table cell borders in ..bibliography:: directive output */ +table.docutils.citation, table.docutils.citation td, table.docutils.citation th { + border: none; + /* Below needed in some edge cases; if not applied, bottom shadows appear */ + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + + +/* relbar */ + +.related { + line-height: 30px; + width: 100%; + font-size: 0.9rem; +} + +.related.top { + border-bottom: 1px solid #EEE; + margin-bottom: 20px; +} + +.related.bottom { + border-top: 1px solid #EEE; +} + +.related ul { + padding: 0; + margin: 0; + list-style: none; +} + +.related li { + display: inline; +} + +nav#rellinks { + float: right; +} + +nav#rellinks li+li:before { + content: "|"; +} + +nav#breadcrumbs li+li:before { + content: "\00BB"; +} + +/* Hide certain items when printing */ +@media print { + div.related { + display: none; + } +} + +img.github { + position: absolute; + top: 0; + border: 0; + right: 0; +} \ No newline at end of file diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 00000000..d9846dac --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,914 @@ +/* + * Sphinx stylesheet -- basic theme. + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin-top: 10px; +} + +ul.search li { + padding: 5px 0; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: inherit; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/_static/custom.css b/_static/custom.css new file mode 100644 index 00000000..2a924f1d --- /dev/null +++ b/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/_static/doctools.js b/_static/doctools.js new file mode 100644 index 00000000..0398ebb9 --- /dev/null +++ b/_static/doctools.js @@ -0,0 +1,149 @@ +/* + * Base JavaScript utilities for all Sphinx HTML documentation. + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 00000000..7e4c114f --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 00000000..a858a410 Binary files /dev/null and b/_static/file.png differ diff --git a/_static/github-banner.svg b/_static/github-banner.svg new file mode 100644 index 00000000..c47d9dc0 --- /dev/null +++ b/_static/github-banner.svg @@ -0,0 +1,5 @@ + + + + + diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 00000000..c7fe6c6f --- /dev/null +++ b/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/_static/minus.png b/_static/minus.png new file mode 100644 index 00000000..d96755fd Binary files /dev/null and b/_static/minus.png differ diff --git a/_static/plus.png b/_static/plus.png new file mode 100644 index 00000000..7107cec9 Binary files /dev/null and b/_static/plus.png differ diff --git a/_static/pygments.css b/_static/pygments.css new file mode 100644 index 00000000..04a41742 --- /dev/null +++ b/_static/pygments.css @@ -0,0 +1,84 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #8f5902; font-style: italic } /* Comment */ +.highlight .err { color: #a40000; border: 1px solid #ef2929 } /* Error */ +.highlight .g { color: #000000 } /* Generic */ +.highlight .k { color: #004461; font-weight: bold } /* Keyword */ +.highlight .l { color: #000000 } /* Literal */ +.highlight .n { color: #000000 } /* Name */ +.highlight .o { color: #582800 } /* Operator */ +.highlight .x { color: #000000 } /* Other */ +.highlight .p { color: #000000; font-weight: bold } /* Punctuation */ +.highlight .ch { color: #8f5902; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #8f5902; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #8f5902 } /* Comment.Preproc */ +.highlight .cpf { color: #8f5902; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #8f5902; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #8f5902; 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font-weight: bold } /* Name.Tag */ +.highlight .nv { color: #000000 } /* Name.Variable */ +.highlight .ow { color: #004461; font-weight: bold } /* Operator.Word */ +.highlight .pm { color: #000000; font-weight: bold } /* Punctuation.Marker */ +.highlight .w { color: #f8f8f8 } /* Text.Whitespace */ +.highlight .mb { color: #990000 } /* Literal.Number.Bin */ +.highlight .mf { color: #990000 } /* Literal.Number.Float */ +.highlight .mh { color: #990000 } /* Literal.Number.Hex */ +.highlight .mi { color: #990000 } /* Literal.Number.Integer */ +.highlight .mo { color: #990000 } /* Literal.Number.Oct */ +.highlight .sa { color: #4e9a06 } /* Literal.String.Affix */ +.highlight .sb { color: #4e9a06 } /* Literal.String.Backtick */ +.highlight .sc { color: #4e9a06 } /* Literal.String.Char */ +.highlight .dl { color: #4e9a06 } /* Literal.String.Delimiter */ +.highlight .sd { color: #8f5902; font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #4e9a06 } /* Literal.String.Double */ +.highlight .se { color: #4e9a06 } /* Literal.String.Escape */ +.highlight .sh { color: #4e9a06 } /* Literal.String.Heredoc */ +.highlight .si { color: #4e9a06 } /* Literal.String.Interpol */ +.highlight .sx { color: #4e9a06 } /* Literal.String.Other */ +.highlight .sr { color: #4e9a06 } /* Literal.String.Regex */ +.highlight .s1 { color: #4e9a06 } /* Literal.String.Single */ +.highlight .ss { color: #4e9a06 } /* Literal.String.Symbol */ +.highlight .bp { color: #3465a4 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #000000 } /* Name.Function.Magic */ +.highlight .vc { color: #000000 } /* Name.Variable.Class */ +.highlight .vg { color: #000000 } /* Name.Variable.Global */ +.highlight .vi { color: #000000 } /* Name.Variable.Instance */ +.highlight .vm { color: #000000 } /* Name.Variable.Magic */ +.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 00000000..2c774d17 --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,632 @@ +/* + * Sphinx JavaScript utilities for the full-text search. + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/genindex.html b/genindex.html new file mode 100644 index 00000000..93c0dd34 --- /dev/null +++ b/genindex.html @@ -0,0 +1,271 @@ + + + + + + + Index — mrrc-hdr-qa documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Index

+ +
+ A + | C + | D + | G + | I + | M + | N + | P + | R + | S + | T + +
+

A

+ + +
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  • + acq2sqlite + +
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+ +

C

+ + + +
+ +

D

+ + + +
+ +

G

+ + + +
+ +

I

+ + +
+ +

M

+ + +
+ +

N

+ + +
+ +

P

+ + +
+ +

R

+ + + +
+ +

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+ ©2024, EH, WF. + + | + Powered by Sphinx 8.1.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 00000000..07a430c0 --- /dev/null +++ b/index.html @@ -0,0 +1,235 @@ + + + + + + + + mrrc-hdr-qa documentation — mrrc-hdr-qa documentation + + + + + + + + + + + + + + + + + + + +
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mrrc-hdr-qa documentation

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Code to parse dicoms into a template database and alert on non-conforming sequences.

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Code

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dcmmeta2tsv

Give a tab separated metadata value line per dicom file.

acq2sqlite

Convert db.txt into a sqlite database.

change_header

Modify DICOM header information to simulate failing QA.

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Overview

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Template

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See acq2sqlite.DBQuery.CONSTS

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Here’s an example for the RewardedAnti task acquisitions in the WPC-8620 project. The ideal template is found finding the most frequent set of repeated key parameters. 150 of the RewardedAnti seqeuences share the same acq_param set, here stored in the sqlite db on rowid=35. But 4 acquisitions (rows in acq) don’t match. In this case all mismatches can be found in TA.

+_images/nonconforming_example.png +
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Parameters

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Dicom tag list

name

tag

desc

Phase

PhaseEncodingDirectionPositive

csa header phase 0/1

iPAT

ImaPATModeText

csa header grappa acceleration

AcqTime

00080032

Acquisition Time like 145446.685000

AcqDate

00080022

like 20241004

SeriesNumber

00200011

REL Series Number

SubID

00100010

patient name

Comments

00204000

REL Image Comments//Unaliased MB3/PE4/LB SENSE1

Operator

00081070

Project

00081030

ID Study Description//Brain^wpc-8620

SequenceName

0008103e

series description

SequenceType

00180024

ACQ Sequence Name

PED_major

00181312

ACQ Phase Encoding Direction ROW or COL

TR

00180080

TE

00180081

Matrix

00181310

ACQ Acquisition Matrix

PixelResol

00280030

IMG Pixel Spacing//2.29787230491642.2978723049164

BWP

00180095

ACQ Pixel Bandwidth (?) also unimplemented? need CSA value?

BWPPE

00191028

in matlab S.BandwidthPerPixelPhaseEncode;

FA

00181314

TA

0051100a

FoV

0051100c

eg FoV 1617*1727; but actually cocaluated from matrix and spacing?

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+ ©2024, EH, WF. + + | + Powered by Sphinx 8.1.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 00000000..fcf974c7 Binary files /dev/null and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 00000000..d3883720 --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,140 @@ + + + + + + + Python Module Index — mrrc-hdr-qa documentation + + + + + + + + + + + + + + + + + + + + + + + +
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Python Module Index

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+ a | + c | + d +
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+ a
+ acq2sqlite +
 
+ c
+ change_header +
 
+ d
+ dcmmeta2tsv +
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+ ©2024, EH, WF. + + | + Powered by Sphinx 8.1.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 00000000..929af5ba --- /dev/null +++ b/search.html @@ -0,0 +1,122 @@ + + + + + + + Search — mrrc-hdr-qa documentation + + + + + + + + + + + + + + + + + + + + + + + + + +
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Search

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+ Searching for multiple words only shows matches that contain + all words. +

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+ ©2024, EH, WF. + + | + Powered by Sphinx 8.1.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 00000000..623df0af --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Code": [[3, "code"]], "Dicom tag list": [[3, "id1"]], "Overview": [[3, "overview"]], "Parameters": [[3, "parameters"]], "Template": [[3, "template"]], "acq2sqlite": [[0, null]], "change_header": [[1, null]], "dcmmeta2tsv": [[2, null]], "mrrc-hdr-qa documentation": [[3, null]]}, "docnames": ["_autosummary/acq2sqlite", "_autosummary/change_header", "_autosummary/dcmmeta2tsv", "index"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["_autosummary/acq2sqlite.rst", "_autosummary/change_header.rst", 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3], "time": [0, 1, 3], "tm": 1, "tr": [0, 2, 3], "track": 0, "true": [0, 2], "try": 0, "tsv": [0, 2], "tsv_to_dict": 0, "tupl": [1, 2], "txt": [0, 2], "type": [0, 1, 2], "unalias": 3, "unimpl": 3, "uniqu": 0, "unless": 1, "us": [0, 1, 2], "valu": [0, 1, 2, 3], "vr": 1, "want": 2, "we": [0, 1], "what": 0, "when": [0, 2], "where": 1, "within": 0, "wpc": [0, 3], "write": 1, "x": [0, 1], "xt": 0, "xx": 1, "yield": 1}, "titles": ["acq2sqlite", "change_header", "dcmmeta2tsv", "mrrc-hdr-qa documentation"], "titleterms": {"acq2sqlit": 0, "change_head": 1, "code": 3, "dcmmeta2tsv": 2, "dicom": 3, "document": 3, "hdr": 3, "list": 3, "mrrc": 3, "overview": 3, "paramet": 3, "qa": 3, "tag": 3, "templat": 3}}) \ No newline at end of file diff --git a/taglist.csv b/taglist.csv new file mode 100644 index 00000000..8c860f63 --- /dev/null +++ b/taglist.csv @@ -0,0 +1,22 @@ +name,tag,desc +Phase,PhaseEncodingDirectionPositive, csa header phase 0/1 +iPAT,ImaPATModeText,csa header grappa acceleration +AcqTime,00080032, Acquisition Time like 145446.685000 +AcqDate,00080022, like 20241004 +SeriesNumber,00200011, REL Series Number +SubID,00100010, patient name +Comments,00204000,REL Image Comments//Unaliased MB3/PE4/LB SENSE1 +Operator,00081070 +Project,00081030, ID Study Description//Brain^wpc-8620 +SequenceName,0008103e, series description +SequenceType,00180024, ACQ Sequence Name +PED_major,00181312, ACQ Phase Encoding Direction ROW or COL +TR,00180080 +TE,00180081 +Matrix,00181310, ACQ Acquisition Matrix +PixelResol,00280030, IMG Pixel Spacing//2.2978723049164\2.2978723049164 +BWP,00180095, ACQ Pixel Bandwidth (?) also unimplemented? need CSA value? +BWPPE,00191028, in matlab S.BandwidthPerPixelPhaseEncode; +FA,00181314 +TA,0051100a +FoV,0051100c, eg FoV 1617*1727; but actually cocaluated from matrix and spacing?