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How to use list_volumes method in tempest
Best Python code snippet using tempest_python
Series.py
Source:Series.py 
1import logging2import os3import zipfile4import json5import sys6import pydicom as dicom7import SimpleITK as sitk8import numpy as np9from classes.Volume import Volume10from pydicom.dataset import Dataset, FileDataset11class Series(object):12 series_id = None13 study_id = None14 metrics = None # ?15 image = None16 series_info = None17 loaded = None18 def __init__(self):19 super().__init__()20 self.series_info = dict([21 ('PatientID', 0),22 ('PatientName', 0),23 ('PatientSex', 0),24 ('PatientAge', 0),25 ('PatientBirthDate', 0),26 ('ContentDate', 0),27 ('ContrastBolusAgent', 0),28 ('ContrastBolusRoute', 0),29 ('Manufacturer', 0),30 ('ManufacturerModelName', 0)31 ])32 self.loaded = False33 self.miniature = None34 self.list_volumes = []35 self.path_to_series = ''36 def download_series(self, folder):37 if folder.type == 'pacs':38 self.parse_dataset(folder)39 elif folder.type == 'folder':40 self.from_folder(folder)41 def parse_dataset(self, dt):42 if type(dt) is Dataset:43 try:44 self.image = None45 except Exception as e:46 print(e)47 else:48 print('It not need type')49 def from_folder(self, path_to_series):50 current_path = os.getcwd()51 try:52 self.path_to_series = path_to_series53 series_reader = sitk.ImageSeriesReader()54 os.chdir(path_to_series)55 dicom_files_name = series_reader.GetGDCMSeriesFileNames('./')56 series_reader.SetFileNames(dicom_files_name)57 image = series_reader.Execute()58 os.chdir(current_path)59 meta_info = dicom.read_file('%s/%s' % (path_to_series, dicom_files_name[0]))60 self.meta_load(meta_info)61 self.image = np.array(sitk.GetArrayFromImage(image)[::-1], dtype=np.int16)62 self.series_info.update({'ImagesNumber': len(self.image),63 'ImageShape': self.image.shape[1:]})64 self.miniature = self.image[len(self.image) // 2] // 10 + 10065 self.loaded = True66 if 'series_info.json' in os.listdir(path_to_series):67 self.json_decode()68 except Exception as e:69 os.chdir(current_path)70 print(path_to_series, self.loaded)71 print(e)72 def meta_load(self, meta_data):73 try:74 if type(meta_data) is FileDataset:75 for key, _ in self.series_info.items():76 value = getattr(meta_data, key, '')77 if type(value) not in (str, int, float):78 value = str(value)79 if key == 'ContentDate' or key == 'PatientBirthDate':80 value = '.'.join([value[6:], value[4:6], value[:4]])81 self.series_info.update({key: value})82 x, y = getattr(meta_data, 'PixelSpacing', [1, 1])83 z_t = float(getattr(meta_data, 'SliceThickness', 2))84 z_s = float(getattr(meta_data, 'spacingBetweenSlices', 0))85 self.metrics = np.array([z_t + z_s, float(y), float(x)])86 self.series_info.update({'SliceThickness': z_t})87 self.series_id = getattr(meta_data, 'SeriesInstanceUID', -1)88 self.study_id = getattr(meta_data, 'StudyInstanceUID', -1)89 except Exception as e:90 print(e)91 def add_value(self, coordinate, size=None, type_volume=None, probability=None, is_doctor=False, is_confirmed=False):92 if coordinate is not None:93 try:94 self.list_volumes.append(Volume(coordinate, size, type_volume, probability, is_doctor, is_confirmed))95 except Exception as e:96 print('add_value', e)97 def get_series_info(self):98 return self.series_info99 def get_metric(self):100 return self.metrics101 def get_image(self):102 return self.image103 def get_study_id(self):104 return self.study_id105 def get_series_id(self):106 return self.series_id107 def get_status(self):108 return self.loaded109 def get_miniature(self):110 return self.miniature111 def get_list_contour_from_doctor(self):112 return [volume.get_coordinate() for volume in self.list_volumes if volume.is_doctor]113 def get_volume_size(self, coordinate):114 try:115 point_number = len(np.argwhere(self.image[coordinate[0, 0]:coordinate[1, 0],116 coordinate[0, 1]:coordinate[1, 1],117 coordinate[0, 2]:coordinate[1, 2]] > -150))118 point_number *= self.metrics.prod()119 return int(point_number)120 except Exception as e:121 print(e, 'get_volume_size')122 def get_volume_from_point(self, z, x, y):123 for volume in self.list_volumes:124 if volume.is_point_in_coordinate(z, x, y):125 return volume.json_code()126 def delete_volume_from_point(self, z, x, y):127 for volume, i in zip(self.list_volumes, range(len(self.list_volumes))):128 if volume.is_point_in_coordinate(z, x, y):129 self.list_volumes.pop(i)130 def save_series(self):131 try:132 if self.path_to_series != '':133 jsonfile = open(self.path_to_series + '/series_info.json', 'w')134 json.dump(self.json_code(), jsonfile)135 return True136 else:137 return False138 except Exception as e:139 print(e, 'save_series')140 return False141 def series_to_send_zip(self):142 current_dir = os.getcwd()143 try:144 zipf = zipfile.ZipFile('tmp/%s.zip' % self.series_id, 'w', zipfile.ZIP_DEFLATED)145 self.save_series()146 os.chdir(self.path_to_series)147 for file in os.listdir(self.path_to_series):148 if '.dcm' in file or '.json' in file:149 zipf.write(file)150 zipf.close()151 os.chdir(current_dir)152 return 'tmp/%s.zip' % self.series_id153 except Exception as e:154 os.chdir(current_dir)155 print(e, 'series_to_send_zip')156 def json_code(self):157 try:158 list_volumes = [volume.json_code() for volume in self.list_volumes]159 file = {160 'Type': 'series',161 'SeriesID': self.series_id,162 'StudyID': self.study_id,163 'Information': self.series_info,164 'Metrics': self.metrics.tolist(),165 'Volumes': list_volumes166 }167 return file168 except Exception as e:169 print(e, 'json_code')170 return None171 def json_decode(self):172 try:173 file_name = '%s/series_info.json' % self.path_to_series174 with open(file_name, 'r') as json_file:175 file = json.load(json_file)176 self.series_from_dict(file)177 except Exception as e:178 print(e, 'json_decode')179 def series_from_dict(self, file):180 try:181 # self.series_id = file['SeriesID']182 # self.study_id = file['StudyID']183 # self.series_info = file['Information']184 self.metrics = np.array(file['Metrics'])185 list_volume = file['Volumes']186 for volume in list_volume:187 try:188 self.add_value(volume['coordinate'], volume['volume_size'], volume['volume_type'],189 volume['probability'], volume['is_doctor'], volume['is_confirmed'])190 if volume['information'] != dict([]):191 self.list_volumes[-1].set_information(volume['information'])192 except Exception as e:193 print(e, 'series_from_dict, for')194 except Exception as e:...
Launcher.py
Source:Launcher.py
1import os2import sys3import docker4from PyQt5.QtWidgets import QVBoxLayout, QHBoxLayout, QLabel, QLineEdit, QPushButton, QListWidget, QFileDialog, \5 QMainWindow, QWidget, QListWidgetItem, QApplication6from PyQt5.QtCore import Qt7class Launcher(QMainWindow):8 def __init__(self):9 super().__init__()10 self.setWindowTitle("dti_launcher")11 self.main_layout = MainLayout(self)12 self.setCentralWidget(self.main_layout)13 self.setGeometry(100, 100, 500, 500)14 self.show()15class MainLayout(QWidget):16 def __init__(self, parent):17 super().__init__(parent)18 self.volumes = dict()19 layout = QVBoxLayout(self)20 # X Server IP21 lbl_ip = QLabel(self)22 lbl_ip.setText("X-Server IP address")23 layout.addWidget(lbl_ip)24 ip_layout = QHBoxLayout(self)25 self.txt_ip_1 = self.add_text_ip("172", 3)26 ip_layout.addWidget(self.txt_ip_1)27 ip_layout.addWidget(QLabel(".", self))28 self.txt_ip_2 = self.add_text_ip("20", 3)29 ip_layout.addWidget(self.txt_ip_2)30 ip_layout.addWidget(QLabel(".", self))31 self.txt_ip_3 = self.add_text_ip("140", 3)32 ip_layout.addWidget(self.txt_ip_3)33 ip_layout.addWidget(QLabel(".", self))34 self.txt_ip_4 = self.add_text_ip("113", 3)35 ip_layout.addWidget(self.txt_ip_4)36 ip_layout.addWidget(QLabel(":", self))37 self.txt_ip_5 = self.add_text_ip("0", 4)38 ip_layout.addWidget(self.txt_ip_5)39 ip_layout.addWidget(QLabel(".", self))40 self.txt_ip_6 = self.add_text_ip("0", 4)41 ip_layout.addWidget(self.txt_ip_6)42 ip_layout.addStretch()43 layout.addLayout(ip_layout)44 # volume mapping45 layout.addStretch()46 layout.addWidget(QLabel("Volume mapping", self))47 host_layout = QHBoxLayout(self)48 host_layout.addWidget(QLabel("Host: ", self))49 self.txt_host = QLineEdit("", self)50 self.txt_host.setReadOnly(True)51 host_layout.addWidget(self.txt_host)52 self.btn_get_folder = QPushButton(self)53 self.btn_get_folder.setText("Get")54 self.btn_get_folder.clicked.connect(self.get_folder)55 host_layout.addWidget(self.btn_get_folder)56 layout.addLayout(host_layout)57 docker_layout = QHBoxLayout(self)58 docker_layout.addWidget(QLabel("Docker: ", self))59 self.txt_docker = QLineEdit("/mnt/data", self)60 self.txt_docker.setReadOnly(True)61 docker_layout.addWidget(self.txt_docker)62 layout.addLayout(docker_layout)63 self.btn_add = QPushButton(self)64 self.btn_add.setText("Add")65 self.btn_add.clicked.connect(self.add_folder)66 layout.addWidget(self.btn_add)67 self.btn_rem = QPushButton(self)68 self.btn_rem.setText("Remove")69 self.btn_rem.clicked.connect(self.rem_folder)70 layout.addWidget(self.btn_rem)71 self.list_volumes = QListWidget(self)72 layout.addWidget(self.list_volumes)73 lbl_list = QLabel("data folder on host computer || data folder in the docker container")74 lbl_list.setAlignment(Qt.AlignCenter)75 layout.addWidget(lbl_list)76 # Launch Button77 self.btn_launch = QPushButton(self)78 self.btn_launch.setText("Launch")79 self.btn_launch.clicked.connect(self.launch)80 layout.addStretch()81 layout.addWidget(self.btn_launch)82 self.setLayout(layout)83 def add_text_ip(self, string, max_length):84 txt_ip = QLineEdit(string, self)85 txt_ip.setMaxLength(max_length)86 txt_ip.setFixedWidth(40)87 txt_ip.setAlignment(Qt.AlignCenter)88 return txt_ip89 def get_folder(self):90 dlg = QFileDialog(self)91 dlg.setFileMode(QFileDialog.Directory)92 dlg.setWindowTitle("Select data directory")93 if dlg.exec_():94 files = dlg.selectedFiles()95 if self.validate_host_dir(files[0]):96 self.txt_host.setText(files[0])97 @staticmethod98 def validate_host_dir(directory):99 if os.path.isdir(directory):100 return True101 else:102 return False103 def add_folder(self):104 if self.validate_host_dir(self.txt_host.text()):105 item = QListWidgetItem()106 item.setTextAlignment(Qt.AlignCenter)107 if self.txt_docker.text()[0] != "/":108 self.txt_docker.setText("/" + self.txt_docker.text())109 item.setText(self.txt_host.text() + " || " + self.txt_docker.text())110 self.list_volumes.addItem(item)111 self.txt_host.setText("")112 self.txt_host.setReadOnly(False)113 self.txt_docker.setText("")114 self.txt_docker.setReadOnly(False)115 def rem_folder(self):116 for item in self.list_volumes.selectedItems():117 self.list_volumes.takeItem(self.list_volumes.row(item))118 if self.list_volumes.count() == 0:119 self.txt_docker.setText("/mnt/data")120 self.txt_docker.setReadOnly(True)121 def launch(self):122 display_env = ["DISPLAY=" + self.txt_ip_1.text() + "."123 + self.txt_ip_2.text() + "." + self.txt_ip_3.text() + "."124 + self.txt_ip_4.text() + ":"125 + self.txt_ip_5.text() + "." + self.txt_ip_6.text(), 'USER=neuro']126 volumes = dict()127 for count in range(self.list_volumes.count()):128 str_split = self.list_volumes.item(count).text().split(" || ")129 volumes[str_split[0]] = {'bind': str_split[1], 'mode': 'rw'}130 # add Scripts folder131 curr_path = os.path.abspath(__file__)132 volumes[os.path.split(curr_path)[0]] = {'bind': '/mnt/scripts/', 'mode': 'rw'}133 # docker client134 client = docker.from_env()135 ctnr = client.containers.run(image='sachslab/dti_base:0.3f', environment=display_env,136 command='python /mnt/scripts/Main/Main.py', detach=True, tty=True,137 volumes=volumes, remove=True)138 # Closing launcher window139 self.parent().close()140if __name__ == '__main__':141 qapp = QApplication(sys.argv) # application object / sys.argv are command line arguments.142 aw = Launcher() # basic widget creation, if no parent: widget == window...
test_list_task_output.py
Source:test_list_task_output.py
1import mock2import unittest3import kojihub4class TestListTaskOutput(unittest.TestCase):5 @mock.patch('os.path.isdir')6 @mock.patch('os.walk')7 def test_empty(self, walk, isdir):8 isdir.return_value = True9 walk.return_value = []10 result = kojihub.list_task_output(1)11 self.assertEqual(result, [])12 @mock.patch('os.path.isdir')13 @mock.patch('os.walk')14 def test_simple(self, walk, isdir):15 isdir.return_value = True16 walk.return_value = (('dir', [], ['file']),)17 result = kojihub.list_task_output(1)18 self.assertEqual(result, ['file'])19 @mock.patch('os.stat')20 @mock.patch('os.path.isdir')21 @mock.patch('os.walk')22 def test_simple_stat(self, walk, isdir, stat):23 isdir.return_value = True24 walk.return_value = (('dir', [], ['file']),)25 st_mock = mock.MagicMock()26 st_mock.st_size = 12327 st_mock.st_atime = 34528 st_mock.st_mtime = 67829 st_mock.st_ctime = 90130 stat.return_value = st_mock31 result = kojihub.list_task_output(1, stat=True)32 self.assertEqual(result, {33 'file': {34 'st_size': '123',35 'st_atime': 345,36 'st_mtime': 678,37 'st_ctime': 901,38 }39 })40 @mock.patch('kojihub.list_volumes')41 @mock.patch('os.stat')42 @mock.patch('os.path.isdir')43 @mock.patch('os.walk')44 def test_volumes(self, walk, isdir, stat, list_volumes):45 isdir.return_value = True46 walk.return_value = (('dir', [], ['file']),)47 st_mock = mock.MagicMock()48 st_mock.st_size = 12349 st_mock.st_atime = 34550 st_mock.st_mtime = 67851 st_mock.st_ctime = 90152 stat.return_value = st_mock53 list_volumes.return_value = [{'name': 'DEFAULT'}]54 result = kojihub.list_task_output(1, all_volumes=True)55 self.assertEqual(result, {'file': ['DEFAULT']})56 @mock.patch('kojihub.list_volumes')57 @mock.patch('os.stat')58 @mock.patch('os.path.isdir')59 @mock.patch('os.walk')60 def test_volumes_stat(self, walk, isdir, stat, list_volumes):61 isdir.return_value = True62 walk.return_value = (('dir', [], ['file']),)63 st_mock = mock.MagicMock()64 st_mock.st_size = 12365 st_mock.st_atime = 34566 st_mock.st_mtime = 67867 st_mock.st_ctime = 90168 stat.return_value = st_mock69 list_volumes.return_value = [{'name': 'DEFAULT'}]70 result = kojihub.list_task_output(1, stat=True, all_volumes=True)71 self.assertEqual(result, {72 'file': {73 'DEFAULT': {74 'st_size': '123',75 'st_atime': 345,76 'st_mtime': 678,77 'st_ctime': 901,78 }79 }...
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