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Update API summary header and qc too grep more info #4077

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merged 10 commits into from
Feb 4, 2019
Merged

Update API summary header and qc too grep more info #4077

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c3a6972
Added Scanner information to the summary headers of the API
cmadjar Nov 7, 2018
14a5f25
Fixed the QC query at the file level and added query of the reason fo…
cmadjar Nov 7, 2018
2c78b9c
Taking care of Travis' error
cmadjar Nov 8, 2018
c300c0f
Mélanie's feedback
cmadjar Nov 12, 2018
9b48798
fixed Travis errors
cmadjar Nov 12, 2018
e616abd
renamed variables to start with lower case in Headers.php of API v0.0.3
cmadjar Nov 12, 2018
fa438c5
John's feedback on array declaration
cmadjar Nov 12, 2018
96f5246
Fixed Travis error
cmadjar Nov 19, 2018
ef40a59
added the new fields in the API documentation
cmadjar Jan 10, 2019
ec41a3d
Dave feedback
cmadjar Jan 14, 2019
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27 changes: 25 additions & 2 deletions docs/API/LorisRESTAPI_v0.0.3.md
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Original file line number Diff line number Diff line change
Expand Up @@ -581,7 +581,23 @@ Returns file level QC information. It will return a JSON object of the form:
"File" : $Filename
},
"QC" : "Pass|Fail",
"Selected" : boolean
"Selected" : boolean,
"Caveats" : [
{
"Severity" : $severity,
"Header" : $header,
"Value" : $headerValue,
"ValidRange" : $headerValidRange,
"ValidRegex" : $headerValidRegex
},
{
"Severity" : $severity,
"Header" : $header,
"Value" : $headerValue,
"ValidRange" : $headerValidRange,
"ValidRegex" : $headerValidRegex
}
]
}
```

Expand Down Expand Up @@ -668,7 +684,7 @@ will return a JSON object of the form:
"Description" : {
"SeriesName" : "",
"SeriesDescription" : ""
}
},
"Dimensions" : {
"XSpace" : {
"Length" : "",
Expand All @@ -686,6 +702,13 @@ will return a JSON object of the form:
"Length" : "",
"StepSize" : ""
}
},
"ScannerInfo" : {
"Manufacturer" : $scannerManufacturer,
"Model" : $scannerModel,
"SoftwareVersion" : $scannerSoftwareVersion,
"SerialNumber" : $scannerSerialNumber,
"FieldStrength" : $scannerFieldStrength
}
}
```
Expand Down
14 changes: 7 additions & 7 deletions htdocs/api/v0.0.2/candidates/visits/images/qc/QC.php
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Original file line number Diff line number Diff line change
Expand Up @@ -64,13 +64,13 @@ public function handleGET()
$factory = \NDB_Factory::singleton();
$DB = $factory->Database();
$QCStatus = $DB->pselectRow(
"SELECT QCStatus,
pf.Value as Selected FROM files f
LEFT JOIN files_qcstatus fqc ON (f.FileID=fqc.FileID)
LEFT JOIN parameter_file pf ON (f.FileID=pf.FileID)
LEFT JOIN parameter_type pt
ON (pf.ParameterTypeID=pt.ParameterTypeID AND pt.Name='Selected')
WHERE f.File LIKE CONCAT('%', :FName)",
"SELECT QCStatus, Selected
FROM files_qcstatus
WHERE FileID in (
SELECT FileID
FROM files
WHERE File LIKE CONCAT('%', :FName)
)",
array('FName' => $this->Filename)
);
$this->JSON = [
Expand Down
99 changes: 56 additions & 43 deletions htdocs/api/v0.0.3-dev/candidates/visits/images/headers/Headers.php
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Original file line number Diff line number Diff line change
Expand Up @@ -62,54 +62,67 @@ public function __construct($method, $CandID, $VisitLabel, $Filename)
*/
public function handleGET()
{
$TE = $this->getHeader('acquisition:echo_time');
$TR = $this->getHeader('acquisition:repetition_time');
$TI = $this->getHeader('acquisition:inversion_time');
$ST = $this->getHeader('acquisition:slice_thickness');
$te = $this->getHeader('acquisition:echo_time');
$tr = $this->getHeader('acquisition:repetition_time');
$ti = $this->getHeader('acquisition:inversion_time');
$st = $this->getHeader('acquisition:slice_thickness');

$SeriesName = $this->getHeader("acquisition:protocol");
$SeriesDescription = $this->getHeader("acquisition:series_description");
$seriesName = $this->getHeader("acquisition:protocol");
$seriesDescription = $this->getHeader("acquisition:series_description");

$XSpace = [
"Length" => $this->getHeader("xspace:length"),
"StepSize" => $this->getHeader("xspace:step"),
];
$YSpace = [
"Length" => $this->getHeader("yspace:length"),
"StepSize" => $this->getHeader("yspace:step"),
];
$ZSpace = [
"Length" => $this->getHeader("zspace:length"),
"StepSize" => $this->getHeader("zspace:step"),
];
$TimeD = [
"Length" => $this->getHeader("time:length"),
"StepSize" => $this->getHeader("time:step"),
];
$this->JSON = [
'Meta' => [
$xspace = array(
"Length" => $this->getHeader("xspace:length"),
"StepSize" => $this->getHeader("xspace:step"),
);
$yspace = array(
"Length" => $this->getHeader("yspace:length"),
"StepSize" => $this->getHeader("yspace:step"),
);
$zspace = array(
"Length" => $this->getHeader("zspace:length"),
"StepSize" => $this->getHeader("zspace:step"),
);
$timeD = array(
"Length" => $this->getHeader("time:length"),
"StepSize" => $this->getHeader("time:step"),
);

$manufacturer = $this->getHeader("study:manufacturer");
$model = $this->getHeader("study:device_model");
$softwareVersion = $this->getHeader("study:software_version");
$serialNumber = $this->getHeader("study:serial_no");
$fieldStrength = $this->getHeader("study:field_value");

$this->JSON = array(
'Meta' => array(
'CandID' => $this->CandID,
'Visit' => $this->VisitLabel,
'Filename' => $this->Filename,
],
'Physical' => [
"TE" => $TE,
"TR" => $TR,
"TI" => $TI,
"SliceThickness" => $ST,
],
'Description' => [
"SeriesName" => $SeriesName,
"SeriesDescription" => $SeriesDescription,
],
'Dimensions' => [
"XSpace" => $XSpace,
"YSpace" => $YSpace,
"ZSpace" => $ZSpace,
"TimeDimension" => $TimeD,
],

];
),
'Physical' => array(
"TE" => $te,
"TR" => $tr,
"TI" => $ti,
"SliceThickness" => $st,
),
'Description' => array(
"SeriesName" => $seriesName,
"SeriesDescription" => $seriesDescription,
),
'Dimensions' => array(
"XSpace" => $xspace,
"YSpace" => $yspace,
"ZSpace" => $zspace,
"TimeDimension" => $timeD,
),
'ScannerInfo' => array(
"Manufacturer" => $manufacturer,
"Model" => $model,
"SoftwareVersion" => $softwareVersion,
"SerialNumber" => $serialNumber,
"FieldStrength" => $fieldStrength,
),
);
}

/**
Expand Down
43 changes: 32 additions & 11 deletions htdocs/api/v0.0.3-dev/candidates/visits/images/qc/QC.php
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Original file line number Diff line number Diff line change
Expand Up @@ -64,24 +64,45 @@ public function handleGET()
$factory = \NDB_Factory::singleton();
$DB = $factory->Database();
$QCStatus = $DB->pselectRow(
"SELECT QCStatus,
pf.Value as Selected FROM files f
LEFT JOIN files_qcstatus fqc ON (f.FileID=fqc.FileID)
LEFT JOIN parameter_file pf ON (f.FileID=pf.FileID)
LEFT JOIN parameter_type pt
ON (pf.ParameterTypeID=pt.ParameterTypeID AND pt.Name='Selected')
WHERE f.File LIKE CONCAT('%', :FName)",
"SELECT QCStatus, Selected
FROM files_qcstatus
WHERE FileID in (
SELECT FileID
FROM files
WHERE File LIKE CONCAT('%', :FName)
)",
array('FName' => $this->Filename)
);
$this->JSON = [
'Meta' => [
$caveats = $this->getImageCaveats();
$this->JSON = array(
'Meta' => array(
'CandID' => $this->CandID,
'Visit' => $this->VisitLabel,
'File' => $this->Filename,
],
),
'QC' => $QCStatus['QCStatus'],
'Selected' => $QCStatus['Selected'],
];
'Caveats' => $caveats,
);
}

/**
* Gets the list of Caveats for the file.
*
* @return array A list of caveats for the file
*/
function getImageCaveats(): array
{
$factory = \NDB_Factory::singleton();
$DB = $factory->Database();
$rows = $DB->pselect(
"SELECT Severity, Header, Value, ValidRange, ValidRegex
FROM files f
LEFT JOIN mri_violations_log mvl ON (f.SeriesUID=mvl.SeriesUID)
WHERE f.File LIKE CONCAT('%', :FName)",
array('FName' => $this->Filename)
);
return $rows;
}

/**
Expand Down