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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