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_
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A
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B
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C
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D
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E
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F
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H
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I
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L
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M
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N
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P
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Q
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R
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S
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T
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U
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V
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W
_
__init__() (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)
B
base_dir (qipipe.pipeline.workflow_base.WorkflowBase attribute)
bolus_arrival_index() (in module qipipe.helpers.bolus_arrival)
BolusArrivalError
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)
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)
create_profile() (in module qipipe.helpers.metadata)
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)
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)
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)
EXCLUDED_OPTS (in module qipipe.helpers.metadata)
extract_trailing_number() (in module qipipe.qiprofile.parse)
F
FALSE_REGEX (in module qipipe.qiprofile.parse)
fix_dicom_headers() (in module qipipe.staging.fix_dicom)
H
HORMONES (in module qipipe.qiprofile.breast_pathology)
I
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
lesion (qipipe.staging.roi.LesionROI attribute)
LesionROI (class in qipipe.staging.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)
M
map_ctp() (in module qipipe.staging.map_ctp)
MAP_FMT (qipipe.staging.map_ctp.CTPPatientIdMap attribute)
MASK_FILE (in module qipipe.helpers.constants)
MASK_RESOURCE (in module qipipe.helpers.constants)
MetadataError
MODULE_PREFIX_PAT (qipipe.pipeline.workflow_base.WorkflowBase attribute)
MSG_FMT (qipipe.staging.map_ctp.CTPPatientIdMap attribute)
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)
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
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.command (module)
qipipe.helpers.constants (module)
qipipe.helpers.distributable (module)
qipipe.helpers.image (module)
qipipe.helpers.logging (module)
qipipe.helpers.metadata (module)
qipipe.pipeline (module)
qipipe.pipeline.pipeline_error (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.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.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)
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)
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)
scan (qipipe.staging.iterator.VisitIterator attribute)
SCAN_TS_BASE (in module qipipe.helpers.constants)
SCAN_TS_FILE (in module qipipe.helpers.constants)
scan_types (qipipe.staging.image_collection.Collection 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)
skip_existing (qipipe.staging.iterator.VisitIterator attribute)
slice (qipipe.staging.roi.LesionROI attribute)
sort() (in module qipipe.staging.sort)
SOURCE_PAT (qipipe.staging.map_ctp.CTPPatientIdMap attribute)
SUBJECT_FMT (in module qipipe.helpers.constants)
T
T1_PAT (in module qipipe.staging.ohsu)
TRAILING_NUM_REGEX (in module qipipe.qiprofile.parse)
TRUE_REGEX (in module qipipe.qiprofile.parse)
TYPE_PARSERS (in module qipipe.qiprofile.parse)
U
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.modeling)
(in module qipipe.qiprofile.radiotherapy)
(in module qipipe.qiprofile.sarcoma_pathology)
(in module qipipe.qiprofile.scan)
(qipipe.qiprofile.dosage.DosageUpdate method)
(qipipe.qiprofile.pathology.PathologyUpdate method)
update_encounter() (qipipe.qiprofile.pathology.PathologyUpdate method)
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_TAG (in module qipipe.staging.ohsu)
W
with_name() (in module qipipe.staging.image_collection)
WorkflowBase (class in qipipe.pipeline.workflow_base)
worksheet (qipipe.qiprofile.xls.Reader attribute)
write() (qipipe.staging.map_ctp.CTPPatientIdMap method)
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