SYMBOL INDEX (492 symbols across 54 files)

FILE: CNN_LSTM/analysis_results.py
  function get_volume (line 20) | def get_volume(gs):
  function get_area (line 23) | def get_area(gs):
  function combined_sample (line 26) | def combined_sample(gs1, gs2):
  function check_in2d (line 56) | def check_in2d(gs1, gs2):
  function get_single_matched_list (line 83) | def get_single_matched_list(org_sample, det_sample):
  function commpare_sample (line 93) | def commpare_sample(org, det):
  function modify_rc (line 106) | def modify_rc(sample6):
  function merge_gd (line 123) | def merge_gd(gd_sample_set):
  function get_dt_scores (line 137) | def get_dt_scores(sample_dt):
  function main (line 146) | def main():

FILE: CNN_LSTM/evaluate.py
  function get_image_dir (line 15) | def get_image_dir(args):
  function get_results (line 22) | def get_results(args, H):
  function main (line 69) | def main():

FILE: CNN_LSTM/make_json.py
  function removeAllPatches (line 33) | def removeAllPatches():
  function skip (line 38) | def skip(event):  #called when the skip button is hit
  function next (line 51) | def next(event):  #called when the next button is hit
  function clear (line 92) | def clear(event): #called when the clear button is hit
  function onclick (line 97) | def onclick(event):  #called when anywhere inside the window is clicked
  function undo (line 109) | def undo(event):  #called when the undo button is hit

FILE: CNN_LSTM/train.py
  function _hungarian_grad (line 32) | def _hungarian_grad(op, *args):
  function build_lstm_inner (line 35) | def build_lstm_inner(H, lstm_input):
  function build_overfeat_inner (line 61) | def build_overfeat_inner(H, lstm_input):
  function deconv (line 74) | def deconv(x, output_shape, channels):
  function rezoom (line 82) | def rezoom(H, pred_boxes, early_feat, early_feat_channels, w_offsets, h_...
  function build_forward (line 125) | def build_forward(H, x, phase, reuse):
  function build_forward_backward (line 237) | def build_forward_backward(H, x, phase, boxes, flags):
  function build (line 310) | def build(H, q):
  function train (line 417) | def train(H, test_images):
  function main (line 526) | def main():

FILE: CNN_LSTM/utils/__init__.py
  function tf_concat (line 7) | def tf_concat(axis, values, **kwargs):

FILE: CNN_LSTM/utils/annolist/AnnotationLib.py
  function cmpAnnoRectsByScore (line 33) | def cmpAnnoRectsByScore(r1, r2):
  function cmpAnnoRectsByScoreDescending (line 36) | def cmpAnnoRectsByScoreDescending(r1, r2):
  function cmpDetAnnoRectsByScore (line 39) | def cmpDetAnnoRectsByScore(r1, r2):
  function suffixMatch (line 43) | def suffixMatch(fn1, fn2):
  class AnnoList (line 55) | class AnnoList(MutableSequence):
    method __init__ (line 61) | def __init__(self, data=None):
    method add_attribute (line 72) | def add_attribute(self, name, dtype):
    method add_attribute_val (line 93) | def add_attribute_val(self, aname, vname, val):
    method attribute_get_value_str (line 111) | def attribute_get_value_str(self, aname, val):
    method save (line 117) | def save(self, fname):
    method __len__ (line 121) | def __len__(self):
    method __getitem__ (line 124) | def __getitem__(self, ii):
    method __delitem__ (line 133) | def __delitem__(self, ii):
    method __setitem__ (line 136) | def __setitem__(self, ii, val):
    method __str__ (line 140) | def __str__(self):
    method __repr__ (line 143) | def __repr__(self):
    method insert (line 146) | def insert(self, ii, val):
    method append (line 149) | def append(self, val):
  function is_compatible_attr_type (line 154) | def is_compatible_attr_type(protobuf_type, attr_type):
  function protobuf_type_to_python (line 165) | def protobuf_type_to_python(protobuf_type):
  class AnnoPoint (line 176) | class AnnoPoint(object):
    method __init__ (line 177) | def __init__(self, x=None, y=None, id=None):
  class AnnoRect (line 182) | class AnnoRect(object):
    method __init__ (line 183) | def __init__(self, x1=-1, y1=-1, x2=-1, y2=-1):
    method width (line 203) | def width(self):
    method height (line 206) | def height(self):
    method centerX (line 209) | def centerX(self):
    method centerY (line 212) | def centerY(self):
    method left (line 215) | def left(self):
    method right (line 218) | def right(self):
    method top (line 221) | def top(self):
    method bottom (line 224) | def bottom(self):
    method forceAspectRatio (line 227) | def forceAspectRatio(self, ratio, KeepHeight = False, KeepWidth = False):
    method clipToImage (line 240) | def clipToImage(self, min_x, max_x, min_y, max_y):
    method printContent (line 250) | def printContent(self):
    method ascii (line 257) | def ascii(self):
    method writeIDL (line 265) | def writeIDL(self, file):
    method writeJSON (line 272) | def writeJSON(self):
    method sortCoords (line 279) | def sortCoords(self):
    method rescale (line 285) | def rescale(self, factor):
    method resize (line 291) | def resize(self, factor, factor_y = None):
    method intersection (line 304) | def intersection(self, other):
    method cover (line 330) | def cover(self, other):
    method overlap_pascal (line 336) | def overlap_pascal(self, other):
    method isMatchingPascal (line 350) | def isMatchingPascal(self, other, minOverlap):
    method distance (line 357) | def distance(self, other, aspectRatio=-1, fixWH='fixheight'):
    method isMatchingStd (line 374) | def isMatchingStd(self, other, coverThresh, overlapThresh, distThresh,...
    method isMatching (line 389) | def isMatching(self, other, style, coverThresh, overlapThresh, distThr...
    method addToXML (line 397) | def addToXML(self, node, doc): # no Silhouette yet
  class Annotation (line 475) | class Annotation(object):
    method __init__ (line 477) | def __init__(self):
    method clone_empty (line 483) | def clone_empty(self):
    method filename (line 491) | def filename(self):
    method printContent (line 494) | def printContent(self):
    method writeIDL (line 499) | def writeIDL(self, file):
    method writeJSON (line 514) | def writeJSON(self):
    method addToXML (line 522) | def addToXML(self, node, doc): # no frame# yet
    method sortByScore (line 542) | def sortByScore(self, dir="ascending"):
    method __getitem__ (line 548) | def __getitem__(self, index):
  class detAnnoRect (line 551) | class detAnnoRect:
    method __init (line 552) | def __init(self):
  function parseTii (line 562) | def parseTii(filename):
  function parseXML (line 613) | def parseXML(filename):
  function parseJSON (line 718) | def parseJSON(filename):
  function parse (line 749) | def parse(filename, abs_path=False):
  function parseIDL (line 775) | def parseIDL(filename):
  function save (line 874) | def save(filename, annotations):
  function saveIDL (line 899) | def saveIDL(filename, annotations):
  function saveJSON (line 922) | def saveJSON(filename, annotations):
  function idlBase (line 933) | def idlBase(filename):
  function saveXML (line 958) | def saveXML(filename, annotations):
  function getStats (line 993) | def getStats(annotations):
  function mergeIDL (line 1072) | def mergeIDL(detIDL, det2IDL, detectionFuse= True, minOverlap = 0.5):
  function forceAspectRatio (line 1114) | def forceAspectRatio(annotations, ratio, KeepHeight = False, KeepWidth =...
  function extractSubSet (line 1144) | def extractSubSet(gtIDL, detIDL):
  function filterMinScore (line 1216) | def filterMinScore(detections, minScore):
  function suffixIdlFileName (line 1233) | def suffixIdlFileName(filename, suffix):
  function annoAnalyze (line 1248) | def annoAnalyze(detIDL):

FILE: CNN_LSTM/utils/annolist/MatPlotter.py
  class MatPlotter (line 13) | class MatPlotter:
    method __init__ (line 27) | def __init__(self, fontsize=15):
    method formatLegend (line 33) | def formatLegend(self, newFontSize = 14, newPlace = 'lower right', bor...
    method newFigure (line 39) | def newFigure(self, plotTitle="", fsize=rcParams['figure.figsize']):
    method newRPCFigure (line 42) | def newRPCFigure(self, plotTitle="", fsize=rcParams['figure.figsize']):
    method newFPPIFigure (line 61) | def newFPPIFigure(self, plotTitle="", fsize=rcParams['figure.figsize']):
    method newFreqFigure (line 80) | def newFreqFigure(self, plotTitle="", maxX = 10, maxY = 10,fsize=rcPar...
    method newFPPWFigure (line 98) | def newFPPWFigure(self, plotTitle="", fsize=rcParams['figure.figsize']):
    method newLogFPPIFigure (line 111) | def newLogFPPIFigure(self, plotTitle="", fsize=rcParams['figure.figsiz...
    method loadRPCData (line 125) | def loadRPCData(self, fname):
    method loadFreqData (line 241) | def loadFreqData(self, fname):
    method loadFPPWData (line 257) | def loadFPPWData(self, fname):
    method finishPlot (line 260) | def finishPlot(self, axlimits = [0,1.0,0,1.0]):
    method finishFreqPlot (line 270) | def finishFreqPlot(self):
    method show (line 276) | def show(self, plotEER = True, axlimits = [0,1.0,0,1.0]):
    method saveCurrentFigure (line 285) | def saveCurrentFigure(self, plotEER, filename, axlimits = [0,1.0,0,1.0]):
    method plotRFP (line 295) | def plotRFP(self, numImages, fname, line="r-"):
    method plotRPC (line 298) | def plotRPC(self, fname, descr="line", style="-1", axlimits = [0,1.0,0...
    method plotFPPI (line 323) | def plotFPPI(self, fname, descr="line", style="-1", axlimits = [0,2,0,...
    method plotFreq (line 345) | def plotFreq(self, fname, descr="line", style="-1", linewidth = 2, das...
    method plotFPPW (line 364) | def plotFPPW(self, fname, descr="line", style="-1", axlimits = [5e-6, ...
    method plotLogFPPI (line 392) | def plotLogFPPI(self, fname, descr="line", style="-1", axlimits = [5e-...

FILE: CNN_LSTM/utils/annolist/PalLib.py
  function loadPal (line 7) | def loadPal(filename):
  function savePal (line 16) | def savePal(filename, _annolist):
  function al2pal (line 21) | def al2pal(annotations):
  function pal2al (line 89) | def pal2al(_annolist):

FILE: CNN_LSTM/utils/annolist/doRPC.py
  function edmonds_karp (line 17) | def edmonds_karp(n, C, s, t, sumC):
  class AnnoGraph (line 50) | class AnnoGraph:
    method __init__ (line 52) | def __init__(self, anno, det, ignore, style, minCover, minOverlap, max...
    method match (line 116) | def match(self, style, minCover, minOverlap, maxDistance):
    method decreaseScore (line 133) | def decreaseScore(self, score):
    method addBB (line 149) | def addBB(self, rect):
    method insertIntoC (line 161) | def     insertIntoC(self, i):
    method maxflow (line 173) | def maxflow(self):
    method consideredDets (line 176) | def consideredDets(self):
    method ignoredFlow (line 179) | def ignoredFlow(self):
    method getTruePositives (line 182) | def getTruePositives(self):
    method getIgnoredTruePositives (line 196) | def getIgnoredTruePositives(self):
    method getMissingRecall (line 210) | def getMissingRecall(self):
    method getFalsePositives (line 218) | def getFalsePositives(self):
  function asort (line 226) | def asort(idlGT, idlDet, minWidth, minHeight, style, minCover, minOverla...
  function comp_prec_recall (line 310) | def comp_prec_recall(annoIDL, detIDL, minOverlap):
  function comp_prec_recall_graphs (line 318) | def comp_prec_recall_graphs(annoIDL, detIDL, minOverlap):
  function comp_prec_recall_all_params (line 328) | def comp_prec_recall_all_params(annoIDL, detIDL, ignoreIDL, minWidth=0, ...
  function main (line 462) | def main():

FILE: CNN_LSTM/utils/annolist/ma_utils.py
  function is_number (line 1) | def is_number(s):

FILE: CNN_LSTM/utils/annolist/plotSimple.py
  function main (line 14) | def main(argv):

FILE: CNN_LSTM/utils/data_utils.py
  function annotation_to_h5 (line 10) | def annotation_to_h5(H, a, cell_width, cell_height, max_len):
  function get_cell_grid (line 52) | def get_cell_grid(cell_width, cell_height, region_size):
  function annotation_jitter (line 70) | def annotation_jitter(I, a_in, min_box_width=20, jitter_scale_min=0.9, j...

FILE: CNN_LSTM/utils/googlenet_load.py
  function model (line 5) | def model(x, H, reuse, is_training=True):

FILE: CNN_LSTM/utils/hungarian/hungarian.cc
  class Rect (line 26) | class Rect {
    method Rect (line 35) | explicit Rect(int cx, int cy, int width, int height, float confidence) {
    method Rect (line 44) | Rect(const Rect& other) {
    method overlaps (line 53) | bool overlaps(const Rect& other) const {
    method distance (line 63) | int distance(const Rect& other) const {
    method intersection (line 68) | float intersection(const Rect& other) const {
    method area (line 79) | int area() const {
    method union_area (line 83) | float union_area(const Rect& other) const {
    method iou (line 87) | float iou(const Rect& other) const {
  function hungarian_print_matrix (line 187) | void hungarian_print_matrix(int** C, int rows, int cols) {
  function hungarian_print_assignment (line 200) | void hungarian_print_assignment(hungarian_problem_t* p) {
  function hungarian_print_costmatrix (line 204) | void hungarian_print_costmatrix(hungarian_problem_t* p) {
  function hungarian_print_status (line 208) | void hungarian_print_status(hungarian_problem_t* p) {
  function hungarian_imax (line 218) | int hungarian_imax(int a, int b) {
  function hungarian_init (line 222) | int hungarian_init(hungarian_problem_t* p, int** cost_matrix, int rows, ...
  function hungarian_free (line 278) | void hungarian_free(hungarian_problem_t* p) {
  function hungarian_solve (line 292) | void hungarian_solve(hungarian_problem_t* p)
  class HungarianOp (line 582) | class HungarianOp : public OpKernel {
    method HungarianOp (line 584) | explicit HungarianOp(OpKernelConstruction* context) : OpKernel(context...
    method Compute (line 586) | void Compute(OpKernelContext* context) override {
    method get_assignment (line 699) | vector<int> get_assignment(vector<float> match_cost, vector<float> los...

FILE: CNN_LSTM/utils/hungarian/hungarian.cpp
  function hungarian_print_matrix (line 49) | void hungarian_print_matrix(int** C, int rows, int cols) {
  function hungarian_print_assignment (line 62) | void hungarian_print_assignment(hungarian_problem_t* p) {
  function hungarian_print_costmatrix (line 66) | void hungarian_print_costmatrix(hungarian_problem_t* p) {
  function hungarian_print_status (line 70) | void hungarian_print_status(hungarian_problem_t* p) {
  function hungarian_imax (line 80) | int hungarian_imax(int a, int b) {
  function hungarian_init (line 84) | int hungarian_init(hungarian_problem_t* p, int** cost_matrix, int rows, ...
  function hungarian_free (line 140) | void hungarian_free(hungarian_problem_t* p) {
  function hungarian_solve (line 154) | void hungarian_solve(hungarian_problem_t* p)

FILE: CNN_LSTM/utils/rect.py
  class Rect (line 1) | class Rect(object):
    method __init__ (line 2) | def __init__(self, cx, cy, width, height, confidence):
    method overlaps (line 9) | def overlaps(self, other):
    method distance (line 16) | def distance(self, other):
    method intersection (line 19) | def intersection(self, other):
    method area (line 27) | def area(self):
    method union (line 29) | def union(self, other):
    method iou (line 31) | def iou(self, other):
    method __eq__ (line 33) | def __eq__(self, other):

FILE: CNN_LSTM/utils/slim_nets/inception_v1.py
  function inception_v1_base (line 29) | def inception_v1_base(inputs,
  function inception_v1 (line 248) | def inception_v1(inputs,
  function inception_v1_arg_scope (line 306) | def inception_v1_arg_scope(weight_decay=0.00004,

FILE: CNN_LSTM/utils/slim_nets/resnet_utils.py
  class Block (line 56) | class Block(collections.namedtuple('Block', ['scope', 'unit_fn', 'args'])):
  function subsample (line 69) | def subsample(inputs, factor, scope=None):
  function conv2d_same (line 87) | def conv2d_same(inputs, num_outputs, kernel_size, stride, rate=1, scope=...
  function stack_blocks_dense (line 150) | def stack_blocks_dense(net,
  function resnet_arg_scope (line 237) | def resnet_arg_scope(is_training=True,

FILE: CNN_LSTM/utils/slim_nets/resnet_v1.py
  function bottleneck (line 69) | def bottleneck(inputs, depth, depth_bottleneck, stride, rate=1,
  function resnet_v1 (line 115) | def resnet_v1(inputs,
  function resnet_v1_50 (line 208) | def resnet_v1_50(inputs,
  function resnet_v1_101 (line 231) | def resnet_v1_101(inputs,
  function resnet_v1_152 (line 254) | def resnet_v1_152(inputs,
  function resnet_v1_200 (line 276) | def resnet_v1_200(inputs,

FILE: CNN_LSTM/utils/stitch_rects.cpp
  function filter_rects (line 13) | void filter_rects(const vector<vector<vector<Rect> > >& all_rects,

FILE: CNN_LSTM/utils/stitch_rects.hpp
  class Rect (line 15) | class Rect {
    method Rect (line 24) | explicit Rect(int cx, int cy, int width, int height, float confidence) {
    method Rect (line 33) | Rect(const Rect& other) {
    method overlaps (line 42) | bool overlaps(const Rect& other, float tau) const {
    method distance (line 52) | int distance(const Rect& other) const {
    method intersection (line 57) | float intersection(const Rect& other) const {
    method area (line 68) | int area() const {
    method union_area (line 72) | float union_area(const Rect& other) const {
    method iou (line 76) | float iou(const Rect& other) const {

FILE: CNN_LSTM/utils/train_utils.py
  function rescale_boxes (line 15) | def rescale_boxes(current_shape, anno, target_height, target_width):
  function load_idl_tf (line 27) | def load_idl_tf(idlfile, H, jitter):
  function make_sparse (line 73) | def make_sparse(n, d):
  function load_data_gen (line 78) | def load_data_gen(H, phase, jitter):
  function add_rectangles (line 99) | def add_rectangles(H, orig_image, confidences, boxes, use_stitching=Fals...
  function to_x1y1x2y2 (line 159) | def to_x1y1x2y2(box):
  function intersection (line 168) | def intersection(box1, box2):
  function area (line 179) | def area(box):
  function union (line 184) | def union(box1, box2):
  function iou (line 187) | def iou(box1, box2):
  function to_idx (line 190) | def to_idx(vec, w_shape):
  function interp (line 197) | def interp(w, i, channel_dim):
  function bilinear_select (line 240) | def bilinear_select(H, pred_boxes, early_feat, early_feat_channels, w_of...

FILE: CNN_LSTM/view_weights.py
  function find_all_files (line 12) | def find_all_files(root, suffix=None):
  function main (line 22) | def main():

FILE: api_lidc/annotation2.py
  function find_all_files (line 13) | def find_all_files(root, suffix=None):
  function parse_dir (line 23) | def parse_dir(dirname, outdir, flatten=True, pickle=True):
  function parse_original_xmls (line 45) | def parse_original_xmls(dirname, outdir, pickle=True):
  function parse (line 65) | def parse(xml_filename):
  function parse_header (line 100) | def parse_header(root):
  function parse_nodule (line 120) | def parse_nodule(xml_node):  # xml_node is one unblindedReadNodule
  function parse_non_nodule (line 175) | def parse_non_nodule(xml_node):  # xml_node is one nonNodule
  function flatten_annotation (line 190) | def flatten_annotation(annotation_dict):
  function flatten_nodule (line 204) | def flatten_nodule(nodules, type, result):

FILE: api_lidc/list.py
  function build_parser (line 10) | def build_parser():
  function analyse (line 17) | def analyse(srcpath, dstpath):
  function main (line 28) | def main():

FILE: api_lidc/list2.py
  function build_parser (line 10) | def build_parser():
  function analyse (line 17) | def analyse(srcpath, dstpath):
  function main (line 39) | def main():

FILE: api_lidc/nodule2.py
  function build_parser (line 12) | def build_parser():
  function annotation (line 19) | def annotation(srcpath, dstpath):
  function main (line 121) | def main():

FILE: api_lidc/nodule_structs.py
  class NoduleCharstics (line 6) | class NoduleCharstics:
    method __init__ (line 7) | def __init__(self):
    method __str__ (line 19) | def __str__(self):
    method set_values (line 28) | def set_values(self, sub, inter, calc, spher, lob, spic, tex, malig):
  class NoduleRoi (line 40) | class NoduleRoi:  # is common for nodule and non-nodule
    method __init__ (line 41) | def __init__(self, z_pos=0., sop_uid=''):
    method __str__ (line 51) | def __str__(self):
  class Nodule (line 72) | class Nodule:  # is base class for all nodule types (NormalNodule,
    method __init__ (line 74) | def __init__(self):
    method __str__ (line 79) | def __str__(self):
    method tostring (line 85) | def tostring(self):
  class NoduleAnnotationCluster (line 89) | class NoduleAnnotationCluster():  # to be seen
    method __init__ (line 90) | def __init__(self):
    method compute_centroid (line 103) | def compute_centroid(self):
    method set_convex_hull (line 112) | def set_convex_hull(self):
  class NormalNodule (line 137) | class NormalNodule(Nodule):
    method __init__ (line 138) | def __init__(self):
    method tostring (line 143) | def tostring(self):
  class SmallNodule (line 154) | class SmallNodule(Nodule):
    method __init__ (line 155) | def __init__(self):
    method tostring (line 159) | def tostring(self):
  class NonNodule (line 166) | class NonNodule(Nodule):
    method __init__ (line 167) | def __init__(self):
    method tostring (line 171) | def tostring(self):
  class RadAnnotation (line 178) | class RadAnnotation:
    method __init__ (line 179) | def __init__(self, init=True):
    method is_init (line 191) | def is_init(self):
    method set_init (line 194) | def set_init(self, init):
    method __str__ (line 198) | def __str__(self):
  class AnnotationHeader (line 226) | class AnnotationHeader:
    method __init__ (line 227) | def __init__(
    method __str__ (line 240) | def __str__(self):
  class IdriReadMessage (line 256) | class IdriReadMessage:
    method __init__ (line 257) | def __init__(self):

FILE: api_lidc/read_file.py
  function main (line 6) | def main():

FILE: api_lidc/te.py
  function build_parser (line 10) | def build_parser():
  function analyse (line 17) | def analyse(srcpath, dstpath):
  function main (line 42) | def main():

FILE: api_lidc/test17.py
  function build_parser (line 10) | def build_parser():
  function analyse (line 17) | def analyse(srcpath, dstpath):
  function main (line 44) | def main():

FILE: api_lidc/write_bin_file.py
  function build_parser (line 10) | def build_parser():
  function find_all_files (line 16) | def find_all_files(root, suffix=None):
  function main (line 26) | def main():

FILE: cnn_3d/3d_cnn_lung_detect.py
  class CT_Image (line 16) | class CT_Image(object):
    method __init__ (line 24) | def __init__(self, input_folder, lable_file, zoomrate=1.0):
    method get_valid_patients (line 36) | def get_valid_patients(self, patient_list):
    method get_3d_data (line 44) | def get_3d_data(self, path):
    method process_image (line 50) | def process_image(self, patient):
    method padding_image (line 58) | def padding_image(self, patient):
    method get_max_imageshape (line 62) | def get_max_imageshape(self):
    method get_patient_lable (line 73) | def get_patient_lable(self, patient_list):
    method next_batch (line 78) | def next_batch(self, num):
    method validate_batch (line 86) | def validate_batch(self):
  class CNN_3D (line 92) | class CNN_3D(object):
    method __init__ (line 96) | def __init__(self, ctobj):
    method run (line 99) | def run(self):
    method weight_variable (line 176) | def weight_variable(self, shape):
    method bias_variable (line 181) | def bias_variable(self, shape):
    method conv3d (line 186) | def conv3d(self, x, W):
    method max_pool_2x2x2 (line 191) | def max_pool_2x2x2(self, x):
    method add_conv_layer (line 195) | def add_conv_layer(self, inputs, in_size, out_size, layer):

FILE: cnn_3d/3d_cnn_lung_test.py
  class CT_Image (line 16) | class CT_Image(object):
    method __init__ (line 24) | def __init__(self, input_folder, lable_file, zoomrate=1.0):
    method get_valid_patients (line 36) | def get_valid_patients(self, patient_list):
    method get_3d_data (line 44) | def get_3d_data(self, path):
    method process_image (line 50) | def process_image(self, patient):
    method padding_image (line 58) | def padding_image(self, patient):
    method get_max_imageshape (line 62) | def get_max_imageshape(self):
    method get_patient_lable (line 73) | def get_patient_lable(self, patient_list):
    method next_batch (line 78) | def next_batch(self, num):
    method validate_batch (line 86) | def validate_batch(self):
  class CNN_3D (line 92) | class CNN_3D(object):
    method __init__ (line 96) | def __init__(self, ctobj):
    method run (line 99) | def run(self):
    method weight_variable (line 179) | def weight_variable(self, shape):
    method bias_variable (line 184) | def bias_variable(self, shape):
    method conv3d (line 189) | def conv3d(self, x, W):
    method max_pool_2x2x2 (line 194) | def max_pool_2x2x2(self, x):
    method add_conv_layer (line 198) | def add_conv_layer(self, inputs, in_size, out_size, layer):

FILE: cnn_3d/detect2.py
  class CT_Image (line 15) | class CT_Image(object):
    method __init__ (line 23) | def __init__(self, input_folder, lable_file, zoomrate=1.0):
    method get_valid_patients (line 35) | def get_valid_patients(self, patient_list):
    method get_3d_data (line 43) | def get_3d_data(self, path):
    method process_image (line 49) | def process_image(self, patient):
    method padding_image (line 57) | def padding_image(self, patient):
    method get_max_imageshape (line 62) | def get_max_imageshape(self):
    method get_patient_lable (line 73) | def get_patient_lable(self, patient_list):
    method next_batch (line 78) | def next_batch(self, num):
  class CNN_3D (line 89) | class CNN_3D(object):
    method __init__ (line 93) | def __init__(self, ctobj):
    method run (line 96) | def run(self):
    method weight_variable (line 148) | def weight_variable(self, shape):
    method bias_variable (line 152) | def bias_variable(self, shape):
    method conv3d (line 156) | def conv3d(self, x, W):
    method max_pool_2x2x2 (line 161) | def max_pool_2x2x2(self, x):
    method add_conv_layer (line 165) | def add_conv_layer(self, inputs, in_size, out_size, layer):

FILE: pylung/annotation.py
  function parse_dir (line 14) | def parse_dir(dirname, flatten=True, pickle=True):
  function parse_original_xmls (line 36) | def parse_original_xmls(dirname, pickle=True):
  function parse (line 56) | def parse(xml_filename):
  function parse_header (line 91) | def parse_header(root):
  function parse_nodule (line 111) | def parse_nodule(xml_node):  # xml_node is one unblindedReadNodule
  function parse_non_nodule (line 166) | def parse_non_nodule(xml_node):  # xml_node is one nonNodule
  function flatten_annotation (line 181) | def flatten_annotation(annotation_dict):
  function flatten_nodule (line 194) | def flatten_nodule(nodules, type, result):

FILE: pylung/base.py
  class PyLungError (line 28) | class PyLungError(Exception):
  function _load_lib (line 33) | def _load_lib():
  function check_call (line 69) | def check_call(ret):
  function c_str (line 85) | def c_str(string):
  function c_str (line 99) | def c_str(string):
  function c_array (line 114) | def c_array(ctype, values):
  function ctypes2buffer (line 133) | def ctypes2buffer(cptr, length):
  function ctypes2numpy_shared (line 157) | def ctypes2numpy_shared(cptr, shape):
  function ctypes2docstring (line 184) | def ctypes2docstring(num_args, arg_names, arg_types, arg_descs, remove_d...
  function _notify_shutdown (line 226) | def _notify_shutdown():

FILE: pylung/detector.py
  class NoduleDetector (line 11) | class NoduleDetector(object):
    method __init__ (line 12) | def __init__(self, dicom_image):
    method candidates (line 26) | def candidates(self):
    method _init_candidates (line 29) | def _init_candidates(self):
    method detect (line 38) | def detect(self):
    method get_parenchyma_block (line 46) | def get_parenchyma_block(self):

FILE: pylung/filters/filter.py
  class CandidateFilter (line 1) | class CandidateFilter(object):
    method __init__ (line 2) | def __init__(self, image):
    method _filter (line 5) | def _filter(self, x, y, h, w):
    method filter (line 8) | def filter(self, candidates):

FILE: pylung/filters/parenchyma.py
  function _get_parenchyma_mask (line 10) | def _get_parenchyma_mask(image, threashold):
  class ParenchymaFilter (line 31) | class ParenchymaFilter(CandidateFilter):
    method __init__ (line 35) | def __init__(self, image):
    method _filter (line 39) | def _filter(self, x, y, h, w):

FILE: pylung/filters/vgg.py
  class VGGFilter (line 11) | class VGGFilter(CandidateFilter):
    method __init__ (line 12) | def __init__(self, image):
    method _filter (line 18) | def _filter(self, x, y, h, w):

FILE: pylung/libinfo.py
  function find_lib_path (line 8) | def find_lib_path():

FILE: pylung/models/chest_detect.py
  function read_ct_file (line 13) | def read_ct_file(dicom_file):
  function custom_square (line 27) | def custom_square(n):
  function custom_cross (line 33) | def custom_cross(n):
  function process_matrix (line 41) | def process_matrix(mtx):
  function printMatrix (line 123) | def printMatrix(p1, p2, p3, p4, nfls):
  function get_LUT_value (line 172) | def get_LUT_value(data, window, level):
  function get_dicom_PIL (line 181) | def get_dicom_PIL(dataset):
  function plot_panels (line 236) | def plot_panels(panels):

FILE: pylung/models/test.py
  function hello_world (line 63) | def hello_world():
  function process_serve_chestct (line 68) | def process_serve_chestct():
  function upload (line 116) | def upload():
  function get_label_size (line 152) | def get_label_size(a):
  function thresh (line 155) | def thresh(a, b, max_value, C):
  function block_size (line 158) | def block_size(size):
  function custom_square (line 164) | def custom_square(n):
  function custom_cross (line 169) | def custom_cross(n):
  function get_number_neighbours (line 176) | def get_number_neighbours(mask,block):
  function masked_adaptive_threshold (line 182) | def masked_adaptive_threshold(image,mask,max_value,size,C):
  function motsu (line 192) | def motsu(im,iz):
  function bintoint (line 198) | def bintoint(im, thresh):
  function lpf (line 211) | def lpf(im, s, o, d):
  function lpf2 (line 222) | def lpf2(im, s, o, d):
  function allowed_file (line 237) | def allowed_file(filename):
  function isjpg (line 240) | def isjpg(filename):
  function ispng (line 243) | def ispng(filename):
  function istiff (line 246) | def istiff(filename):
  function isdicom (line 249) | def isdicom(filename):
  function readChestCTFile (line 252) | def readChestCTFile(f):
  function processMatrix (line 266) | def processMatrix(mtx,dim):
  function printMatrix (line 344) | def printMatrix(p1, p2, p3, p4, pfx, nfls):
  function get_LUT_value (line 402) | def get_LUT_value(data, window, level):
  function get_dicom_PIL (line 409) | def get_dicom_PIL(dataset):

FILE: pylung/models/train.py
  function load_data (line 14) | def load_data(batch=None):
  function train (line 28) | def train(batch=0, n_epoch=10, checkpoint=None):
  function main (line 38) | def main():

FILE: pylung/models/vgg_classifier.py
  function load_mat (line 11) | def load_mat():
  function net (line 25) | def net(input_image):
  function classifier (line 66) | def classifier():

FILE: pylung/nodule_structs.py
  class NoduleCharstics (line 6) | class NoduleCharstics:
    method __init__ (line 7) | def __init__(self):
    method __str__ (line 19) | def __str__(self):
    method set_values (line 28) | def set_values(self, sub, inter, calc, spher, lob, spic, tex, malig):
  class NoduleRoi (line 40) | class NoduleRoi:  # is common for nodule and non-nodule
    method __init__ (line 41) | def __init__(self, z_pos=0., sop_uid=''):
    method __str__ (line 51) | def __str__(self):
  class Nodule (line 72) | class Nodule:  # is base class for all nodule types (NormalNodule,
    method __init__ (line 74) | def __init__(self):
    method __str__ (line 79) | def __str__(self):
    method tostring (line 85) | def tostring(self):
  class NoduleAnnotationCluster (line 89) | class NoduleAnnotationCluster():  # to be seen
    method __init__ (line 90) | def __init__(self):
    method compute_centroid (line 103) | def compute_centroid(self):
    method set_convex_hull (line 112) | def set_convex_hull(self):
  class NormalNodule (line 137) | class NormalNodule(Nodule):
    method __init__ (line 138) | def __init__(self):
    method tostring (line 143) | def tostring(self):
  class SmallNodule (line 154) | class SmallNodule(Nodule):
    method __init__ (line 155) | def __init__(self):
    method tostring (line 159) | def tostring(self):
  class NonNodule (line 166) | class NonNodule(Nodule):
    method __init__ (line 167) | def __init__(self):
    method tostring (line 171) | def tostring(self):
  class RadAnnotation (line 178) | class RadAnnotation:
    method __init__ (line 179) | def __init__(self, init=True):
    method is_init (line 191) | def is_init(self):
    method set_init (line 194) | def set_init(self, init):
    method __str__ (line 198) | def __str__(self):
  class AnnotationHeader (line 226) | class AnnotationHeader:
    method __init__ (line 227) | def __init__(
    method __str__ (line 240) | def __str__(self):
  class IdriReadMessage (line 256) | class IdriReadMessage:
    method __init__ (line 257) | def __init__(self):

FILE: pylung/tests/demo.py
  function build_parser (line 12) | def build_parser():
  function selectAnno (line 18) | def selectAnno(srcpath):
  function selectPa (line 39) | def selectPa(srcpath):
  function combine (line 62) | def combine():
  function select (line 73) | def select(length):
  function main (line 89) | def main():

FILE: pylung/tests/main.py
  function build_parser (line 29) | def build_parser():
  function is_in (line 38) | def is_in(centroid, field):
  function parenchyma_cut (line 43) | def parenchyma_cut(dcm_file_path, save_file_path):
  function annotation_cut (line 89) | def annotation_cut(dcm_file_path, save_file_path):
  function annotation_cut2 (line 133) | def annotation_cut2(dcm_file_path, save_file_path):
  function original_view (line 189) | def original_view(srcpath, dstpath):
  function original_view2 (line 205) | def original_view2(srcpath, dstpath):
  function parenchyma_view (line 234) | def parenchyma_view(srcpath, dstpath):
  function annotation_view (line 251) | def annotation_view(srcpath, dstpath):
  function main (line 300) | def main():

FILE: pylung/tests/predict.py
  function train (line 15) | def train():

FILE: pylung/tests/test_detect.py
  class NoduleDetectorTest (line 17) | class NoduleDetectorTest(unittest.TestCase):
    method test_1 (line 18) | def test_1(self):
    method test_2 (line 103) | def test_2(self):
    method test_3 (line 130) | def test_3(self):
    method test_4 (line 158) | def test_4(self):

FILE: pylung/tests/tmp.py
  function annotation_cut (line 1) | def annotation_cut(dcm_file_path, save_file_path):

FILE: pylung/tests/train.py
  function train (line 15) | def train():

FILE: pylung/utils.py
  function floodfill (line 7) | def floodfill(image, start_point, value):
  function switch_pixels (line 27) | def switch_pixels(image, origin_value, value):
  function morphology_open (line 35) | def morphology_open(image):
  function morphology_close (line 42) | def morphology_close(image):
  function gray_to_rgb (line 49) | def gray_to_rgb(image):
  function imsave (line 55) | def imsave(fname, image):
  function dcm_to_gray (line 62) | def dcm_to_gray(image):
  function find_all_files (line 70) | def find_all_files(root, suffix=None):
  function dense_to_one_hot (line 80) | def dense_to_one_hot(labels_dense, num_classes):