qipipe
stable
API Documentation
qipipe
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
_
__init__() (qipipe.helpers.roi.Extent method)
(qipipe.helpers.roi.ExtentSegmentFactory method)
(qipipe.helpers.roi.ROI method)
(qipipe.interfaces.convert_bolero_mask.ConvertBoleroMask method)
(qipipe.interfaces.dce_to_r1.DceToR1 method)
(qipipe.interfaces.fastfit.Fastfit method)
(qipipe.interfaces.sticky_identity.StickyIdentityInterface method)
(qipipe.interfaces.unpack.Unpack method)
(qipipe.interfaces.xnat_find.XNATFind method)
(qipipe.pipeline.mask.MaskWorkflow method)
(qipipe.pipeline.modeling.ModelingWorkflow method)
(qipipe.pipeline.qipipeline.QIPipelineWorkflow method)
(qipipe.pipeline.registration.RegisterImageWorkflow method)
(qipipe.pipeline.registration.RegisterScanWorkflow method)
(qipipe.pipeline.roi.ROIWorkflow method)
(qipipe.pipeline.staging.ScanStagingWorkflow method)
(qipipe.pipeline.staging.VolumeStagingWorkflow method)
(qipipe.pipeline.workflow_base.WorkflowBase method)
(qipipe.qiprofile.breast_pathology.BreastPathologyUpdate method)
(qipipe.qiprofile.dosage.DosageUpdate method)
(qipipe.qiprofile.dosage.DosageWorksheet method)
(qipipe.qiprofile.pathology.PathologyUpdate method)
(qipipe.qiprofile.pathology.PathologyWorksheet method)
(qipipe.qiprofile.sarcoma_pathology.SarcomaPathologyUpdate method)
(qipipe.qiprofile.xls.Reader method)
(qipipe.staging.image_collection.Collection method)
(qipipe.staging.iterator.VisitIterator method)
(qipipe.staging.roi.LesionROI method)
A
add_subjects() (qipipe.staging.map_ctp.CTPPatientIdMap method)
AGENT_DEFAULTS (in module qipipe.qiprofile.radiotherapy)
ANTS_CONF_SECTIONS (in module qipipe.pipeline.registration)
ANTS_INITIALIZER_CONF_SECTION (in module qipipe.pipeline.registration)
associate() (in module qipipe.pipeline.modeling)
B
base_dir (qipipe.pipeline.workflow_base.WorkflowBase attribute)
base_name() (in module qipipe.pipeline.roi)
bolus_arrival_index() (in module qipipe.helpers.bolus_arrival)
BolusArrivalError
boundary (qipipe.helpers.roi.Extent attribute)
bounding_box() (qipipe.helpers.roi.Extent method)
BREAST_DW_PAT (in module qipipe.staging.ohsu)
BREAST_PD_PAT (in module qipipe.staging.ohsu)
BREAST_ROI_PAT (in module qipipe.staging.ohsu)
BREAST_ROI_REGEX (in module qipipe.staging.ohsu)
BREAST_SESSION_REGEX (in module qipipe.staging.ohsu)
BREAST_SUBJECT_REGEX (in module qipipe.staging.ohsu)
BREAST_T2_PAT (in module qipipe.staging.ohsu)
BreastPathologyUpdate (class in qipipe.qiprofile.breast_pathology)
C
CFG_FILE (in module qipipe.staging.sarcoma_config)
COL_ATTRS (in module qipipe.qiprofile.chemotherapy)
(in module qipipe.qiprofile.demographics)
(in module qipipe.qiprofile.pathology)
(in module qipipe.qiprofile.radiotherapy)
(in module qipipe.qiprofile.sarcoma_pathology)
Collection (class in qipipe.staging.image_collection)
collection (qipipe.staging.iterator.VisitIterator attribute)
colorize() (in module qipipe.helpers.colors)
COMMA_DELIM_REGEX (in module qipipe.qiprofile.parse)
COMMENT_PREFIX (in module qipipe.staging.fix_dicom)
CONF_DIR (in module qipipe.helpers.constants)
config_dir (qipipe.pipeline.workflow_base.WorkflowBase attribute)
configuration (qipipe.pipeline.workflow_base.WorkflowBase attribute)
configure() (in module qipipe.helpers.logging)
configure_log() (in module qipipe.helpers.command)
CONTAINER_OPTS (in module qipipe.interfaces.xnat_download)
ConvertBoleroMask (class in qipipe.interfaces.convert_bolero_mask)
Copy (class in qipipe.interfaces.copy)
create() (qipipe.helpers.roi.ExtentSegmentFactory method)
create_lookup_table() (in module qipipe.helpers.colors)
create_profile() (in module qipipe.helpers.metadata)
(in module qipipe.pipeline.modeling)
crop_posterior (qipipe.staging.image_collection.Collection attribute)
ctp_collection_for_name() (in module qipipe.staging.ctp_config)
CTP_FMT (qipipe.staging.map_ctp.CTPPatientIdMap attribute)
CTPPatientIdMap (class in qipipe.staging.map_ctp)
D
DATE_FMT (in module qipipe.staging.fix_dicom)
DceToR1 (class in qipipe.interfaces.dce_to_r1)
default_parsers() (in module qipipe.qiprofile.parse)
DEFAULTS (qipipe.qiprofile.dosage.DosageUpdate attribute)
depict_workflow() (qipipe.pipeline.workflow_base.WorkflowBase method)
discretize() (in module qipipe.helpers.image)
distances (qipipe.helpers.roi.ExtentSegmentFactory attribute)
DISTRIBUTABLE (in module qipipe.helpers.distributable)
DosageUpdate (class in qipipe.qiprofile.dosage)
DosageWorksheet (class in qipipe.qiprofile.dosage)
dry_run (qipipe.pipeline.workflow_base.WorkflowBase attribute)
E
encounter_type() (qipipe.qiprofile.breast_pathology.BreastPathologyUpdate method)
(qipipe.qiprofile.pathology.PathologyUpdate method)
ENCOUNTER_TYPES (in module qipipe.qiprofile.pathology)
exclude_files() (in module qipipe.pipeline.qipipeline)
EXCLUDED_OPTS (in module qipipe.helpers.metadata)
Extent (class in qipipe.helpers.roi)
extent (qipipe.helpers.roi.ROI attribute)
ExtentSegmentFactory (class in qipipe.helpers.roi)
extract_trailing_number() (in module qipipe.qiprofile.parse)
F
FALSE_REGEX (in module qipipe.qiprofile.parse)
Fastfit (class in qipipe.interfaces.fastfit)
FASTFIT_CONF_PROPS (in module qipipe.pipeline.modeling)
FASTFIT_PARAMS_FILE (in module qipipe.pipeline.modeling)
fix_dicom_headers() (in module qipipe.staging.fix_dicom)
FixDicom (class in qipipe.interfaces.fix_dicom)
FSL_CONF_SECTIONS (in module qipipe.pipeline.registration)
FXL_MODEL_PREFIX (in module qipipe.pipeline.modeling)
G
get_aif_shift() (in module qipipe.pipeline.modeling)
get_fit_params() (in module qipipe.pipeline.modeling)
get_r1_0() (in module qipipe.pipeline.modeling)
H
HORMONES (in module qipipe.qiprofile.breast_pathology)
I
input_spec (qipipe.interfaces.sticky_identity.StickyIdentityInterface attribute)
(qipipe.interfaces.unpack.Unpack attribute)
(qipipe.interfaces.xnat_copy.XNATCopy attribute)
instances (qipipe.staging.image_collection.Collection attribute)
INTERFACE_PREFIX_PAT (qipipe.pipeline.workflow_base.WorkflowBase attribute)
is_distributable (qipipe.pipeline.workflow_base.WorkflowBase attribute)
iter_roi() (in module qipipe.staging.roi)
iter_stage() (in module qipipe.staging.iterator)
L
label_map_basename() (in module qipipe.helpers.colors)
lesion (qipipe.staging.roi.LesionROI attribute)
LesionROI (class in qipipe.staging.roi)
load() (in module qipipe.helpers.roi)
load_workbook() (in module qipipe.qiprofile.xls)
location (qipipe.staging.roi.LesionROI attribute)
logger (qipipe.pipeline.workflow_base.WorkflowBase attribute)
logger() (in module qipipe.helpers.logging)
Lookup (class in qipipe.interfaces.lookup)
M
make_baseline() (in module qipipe.pipeline.modeling)
map_ctp() (in module qipipe.staging.map_ctp)
MAP_FMT (qipipe.staging.map_ctp.CTPPatientIdMap attribute)
MapCTP (class in qipipe.interfaces.map_ctp)
MASK_FILE (in module qipipe.helpers.constants)
MASK_FILE_NAME (in module qipipe.interfaces.dce_to_r1)
MASK_RESOURCE (in module qipipe.helpers.constants)
MaskWorkflow (class in qipipe.pipeline.mask)
maximal_slice_index() (qipipe.helpers.roi.ROI method)
MetadataError
MODELING_CONF_FILE (in module qipipe.pipeline.modeling)
MODELING_PREFIX (in module qipipe.pipeline.modeling)
modeling_resource (qipipe.pipeline.qipipeline.QIPipelineWorkflow attribute)
modeling_technique (qipipe.pipeline.qipipeline.QIPipelineWorkflow attribute)
ModelingWorkflow (class in qipipe.pipeline.modeling)
MODULE_PREFIX_PAT (qipipe.pipeline.workflow_base.WorkflowBase attribute)
Move (class in qipipe.interfaces.move)
MriVolCluster (class in qipipe.interfaces.mri_volcluster)
MSG_FMT (qipipe.staging.map_ctp.CTPPatientIdMap attribute)
MULTI_VOLUME_ACTIONS (in module qipipe.pipeline.qipipeline)
MULTI_VOLUME_SCAN_NUMBERS (in module qipipe.staging.ohsu)
N
name (qipipe.staging.image_collection.Collection attribute)
NIPYPE_LOG_DIR_ENV_VAR (in module qipipe.helpers.logging)
normalize() (in module qipipe.helpers.image)
O
OHSU_CONF_SECTIONS (in module qipipe.pipeline.modeling)
OUTPUT_FILE_NAME (in module qipipe.interfaces.dce_to_r1)
output_spec (qipipe.interfaces.fastfit.Fastfit attribute)
(qipipe.interfaces.sticky_identity.StickyIdentityInterface attribute)
(qipipe.interfaces.unpack.Unpack attribute)
P
PARAM_REGEX (in module qipipe.staging.roi)
parse_boolean() (in module qipipe.qiprofile.parse)
parse_list_string() (in module qipipe.qiprofile.parse)
parse_trailing_number() (in module qipipe.qiprofile.parse)
PARSERS (in module qipipe.qiprofile.pathology)
(in module qipipe.qiprofile.sarcoma_pathology)
pathology_content() (qipipe.qiprofile.breast_pathology.BreastPathologyUpdate method)
(qipipe.qiprofile.pathology.PathologyUpdate method)
(qipipe.qiprofile.sarcoma_pathology.SarcomaPathologyUpdate method)
PathologyUpdate (class in qipipe.qiprofile.pathology)
PathologyWorksheet (class in qipipe.qiprofile.pathology)
patterns (qipipe.staging.image_collection.Collection attribute)
PipelineError
points (qipipe.helpers.roi.ExtentSegmentFactory attribute)
Preview (class in qipipe.interfaces.preview)
project (qipipe.pipeline.workflow_base.WorkflowBase attribute)
(qipipe.staging.iterator.VisitIterator attribute)
PROP_FMT (in module qipipe.staging.map_ctp)
property_filename() (in module qipipe.staging.map_ctp)
Q
qipipe.helpers (module)
qipipe.helpers.bolus_arrival (module)
qipipe.helpers.colors (module)
qipipe.helpers.command (module)
qipipe.helpers.constants (module)
qipipe.helpers.distributable (module)
qipipe.helpers.image (module)
qipipe.helpers.logging (module)
qipipe.helpers.metadata (module)
qipipe.helpers.roi (module)
qipipe.interfaces (module)
qipipe.interfaces.compress (module)
qipipe.interfaces.convert_bolero_mask (module)
qipipe.interfaces.copy (module)
qipipe.interfaces.dce_to_r1 (module)
qipipe.interfaces.fastfit (module)
qipipe.interfaces.fix_dicom (module)
qipipe.interfaces.group_dicom (module)
qipipe.interfaces.interface_error (module)
qipipe.interfaces.lookup (module)
qipipe.interfaces.map_ctp (module)
qipipe.interfaces.move (module)
qipipe.interfaces.mri_volcluster (module)
qipipe.interfaces.preview (module)
qipipe.interfaces.reorder_bolero_mask (module)
qipipe.interfaces.sticky_identity (module)
qipipe.interfaces.touch (module)
qipipe.interfaces.uncompress (module)
qipipe.interfaces.unpack (module)
qipipe.interfaces.update_qiprofile (module)
qipipe.interfaces.xnat_copy (module)
qipipe.interfaces.xnat_download (module)
qipipe.interfaces.xnat_find (module)
qipipe.interfaces.xnat_upload (module)
qipipe.pipeline (module)
qipipe.pipeline.mask (module)
qipipe.pipeline.modeling (module)
qipipe.pipeline.pipeline_error (module)
qipipe.pipeline.qipipeline (module)
qipipe.pipeline.registration (module)
qipipe.pipeline.roi (module)
qipipe.pipeline.staging (module)
qipipe.pipeline.workflow_base (module)
qipipe.qiprofile (module)
qipipe.qiprofile.breast_pathology (module)
qipipe.qiprofile.chemotherapy (module)
qipipe.qiprofile.clinical (module)
qipipe.qiprofile.demographics (module)
qipipe.qiprofile.dosage (module)
qipipe.qiprofile.imaging (module)
qipipe.qiprofile.modeling (module)
qipipe.qiprofile.parse (module)
qipipe.qiprofile.pathology (module)
qipipe.qiprofile.radiotherapy (module)
qipipe.qiprofile.sarcoma_pathology (module)
qipipe.qiprofile.scan (module)
qipipe.qiprofile.update (module)
qipipe.qiprofile.xls (module)
qipipe.staging (module)
qipipe.staging.ctp_config (module)
qipipe.staging.fix_dicom (module)
qipipe.staging.image_collection (module)
qipipe.staging.iterator (module)
qipipe.staging.map_ctp (module)
qipipe.staging.ohsu (module)
qipipe.staging.roi (module)
qipipe.staging.sarcoma_config (module)
qipipe.staging.sort (module)
qipipe.staging.staging_error (module)
QIPipelineWorkflow (class in qipipe.pipeline.qipipeline)
R
read() (in module qipipe.qiprofile.breast_pathology)
(in module qipipe.qiprofile.chemotherapy)
(in module qipipe.qiprofile.demographics)
(in module qipipe.qiprofile.radiotherapy)
(in module qipipe.qiprofile.sarcoma_pathology)
(qipipe.qiprofile.xls.Reader method)
Reader (class in qipipe.qiprofile.xls)
REG_PREFIX (in module qipipe.pipeline.registration)
RegisterImageWorkflow (class in qipipe.pipeline.registration)
RegisterScanWorkflow (class in qipipe.pipeline.registration)
registration_resource (qipipe.pipeline.qipipeline.QIPipelineWorkflow attribute)
registration_technique (qipipe.pipeline.qipipeline.QIPipelineWorkflow attribute)
reorder_bolero_mask() (in module qipipe.helpers.roi)
ReorderBoleroMask (class in qipipe.interfaces.reorder_bolero_mask)
resource (qipipe.pipeline.modeling.ModelingWorkflow attribute)
(qipipe.pipeline.registration.RegisterScanWorkflow attribute)
ROI (class in qipipe.helpers.roi)
ROI_FNAME_PAT (in module qipipe.pipeline.roi)
ROI_RESOURCE (in module qipipe.pipeline.roi)
ROIWorkflow (class in qipipe.pipeline.roi)
run() (in module qipipe.pipeline.mask)
(in module qipipe.pipeline.modeling)
(in module qipipe.pipeline.qipipeline)
(in module qipipe.pipeline.registration)
(in module qipipe.pipeline.roi)
(in module qipipe.pipeline.staging)
(qipipe.pipeline.mask.MaskWorkflow method)
(qipipe.pipeline.modeling.ModelingWorkflow method)
(qipipe.pipeline.registration.RegisterImageWorkflow method)
(qipipe.pipeline.registration.RegisterScanWorkflow method)
(qipipe.pipeline.roi.ROIWorkflow method)
(qipipe.pipeline.staging.ScanStagingWorkflow method)
(qipipe.pipeline.staging.VolumeStagingWorkflow method)
run_with_dicom_input() (qipipe.pipeline.qipipeline.QIPipelineWorkflow method)
run_with_scan_download() (qipipe.pipeline.qipipeline.QIPipelineWorkflow method)
S
sarcoma_config() (in module qipipe.staging.sarcoma_config)
SARCOMA_DW_PAT (in module qipipe.staging.ohsu)
sarcoma_location() (in module qipipe.staging.sarcoma_config)
SARCOMA_ROI_PAT (in module qipipe.staging.ohsu)
SARCOMA_ROI_REGEX (in module qipipe.staging.ohsu)
SARCOMA_SESSION_REGEX (in module qipipe.staging.ohsu)
SARCOMA_SUBJECT_REGEX (in module qipipe.staging.ohsu)
SARCOMA_T2_PAT (in module qipipe.staging.ohsu)
SarcomaPathologyUpdate (class in qipipe.qiprofile.sarcoma_pathology)
scale (qipipe.helpers.roi.Extent attribute)
scan (qipipe.staging.iterator.VisitIterator attribute)
SCAN_CONF_FILE (in module qipipe.pipeline.staging)
SCAN_METADATA_RESOURCE (in module qipipe.pipeline.staging)
SCAN_TS_BASE (in module qipipe.helpers.constants)
SCAN_TS_FILE (in module qipipe.helpers.constants)
scan_types (qipipe.staging.image_collection.Collection attribute)
ScanStagingWorkflow (class in qipipe.pipeline.staging)
segments (qipipe.helpers.roi.Extent attribute)
session_dirs (qipipe.staging.iterator.VisitIterator attribute)
SESSION_FMT (in module qipipe.helpers.constants)
SESSION_REGEX_PAT (in module qipipe.staging.ohsu)
SHEET (in module qipipe.qiprofile.chemotherapy)
(in module qipipe.qiprofile.demographics)
(in module qipipe.qiprofile.pathology)
(in module qipipe.qiprofile.radiotherapy)
show() (qipipe.helpers.roi.Extent method)
SINGLE_VOLUME_ACTIONS (in module qipipe.pipeline.qipipeline)
skip_existing (qipipe.staging.iterator.VisitIterator attribute)
slice (qipipe.staging.roi.LesionROI attribute)
slices (qipipe.helpers.roi.ROI attribute)
sort() (in module qipipe.staging.sort)
SOURCE_PAT (qipipe.staging.map_ctp.CTPPatientIdMap attribute)
stage_volume() (in module qipipe.pipeline.staging)
StickyIdentityInterface (class in qipipe.interfaces.sticky_identity)
SUBJECT_FMT (in module qipipe.helpers.constants)
T
T1_PAT (in module qipipe.staging.ohsu)
technique (qipipe.pipeline.modeling.ModelingWorkflow attribute)
(qipipe.pipeline.registration.RegisterImageWorkflow attribute)
(qipipe.pipeline.registration.RegisterScanWorkflow attribute)
Touch (class in qipipe.interfaces.touch)
TRAILING_NUM_REGEX (in module qipipe.qiprofile.parse)
TRUE_REGEX (in module qipipe.qiprofile.parse)
TYPE_PARSERS (in module qipipe.qiprofile.parse)
U
Unpack (class in qipipe.interfaces.unpack)
update() (in module qipipe.qiprofile.breast_pathology)
(in module qipipe.qiprofile.chemotherapy)
(in module qipipe.qiprofile.clinical)
(in module qipipe.qiprofile.demographics)
(in module qipipe.qiprofile.imaging)
(in module qipipe.qiprofile.modeling)
(in module qipipe.qiprofile.radiotherapy)
(in module qipipe.qiprofile.sarcoma_pathology)
(in module qipipe.qiprofile.scan)
(in module qipipe.qiprofile.update)
(qipipe.qiprofile.dosage.DosageUpdate method)
(qipipe.qiprofile.pathology.PathologyUpdate method)
update_encounter() (qipipe.qiprofile.pathology.PathologyUpdate method)
UpdateQIProfile (class in qipipe.interfaces.update_qiprofile)
upload_dicom() (in module qipipe.pipeline.staging)
upload_nifti() (in module qipipe.pipeline.staging)
V
VisitIterator (class in qipipe.staging.iterator)
volume (qipipe.staging.roi.LesionROI attribute)
VOLUME_DIR_PAT (in module qipipe.helpers.constants)
VOLUME_FILE_PAT (in module qipipe.helpers.constants)
volume_format() (in module qipipe.pipeline.staging)
VOLUME_TAG (in module qipipe.staging.ohsu)
VolumeStagingWorkflow (class in qipipe.pipeline.staging)
W
with_name() (in module qipipe.staging.image_collection)
workflow (qipipe.pipeline.mask.MaskWorkflow attribute)
(qipipe.pipeline.modeling.ModelingWorkflow attribute)
(qipipe.pipeline.qipipeline.QIPipelineWorkflow attribute)
(qipipe.pipeline.registration.RegisterImageWorkflow attribute)
(qipipe.pipeline.registration.RegisterScanWorkflow attribute)
(qipipe.pipeline.roi.ROIWorkflow attribute)
(qipipe.pipeline.staging.ScanStagingWorkflow attribute)
(qipipe.pipeline.staging.VolumeStagingWorkflow attribute)
WorkflowBase (class in qipipe.pipeline.workflow_base)
worksheet (qipipe.qiprofile.xls.Reader attribute)
write() (qipipe.staging.map_ctp.CTPPatientIdMap method)
X
XNATCopy (class in qipipe.interfaces.xnat_copy)
XNATCopyInputSpec (class in qipipe.interfaces.xnat_copy)
XNATDownload (class in qipipe.interfaces.xnat_download)
XNATFind (class in qipipe.interfaces.xnat_find)
XNATUpload (class in qipipe.interfaces.xnat_upload)
Read the Docs
v: stable
Versions
latest
stable
Downloads
pdf
htmlzip
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.