def __init__(self, *config, db_type='pgsql'):
"""
:param config: optional SQL login credentials, stored values used if nothing provided
:param db_type: either 'pgsql' or 'sqlite'
:type db_type: str
"""
stored_options = Options()
if config:
self.db_type = db_type
config = config[0]
else:
# Read SQL configuration file
self.db_type = stored_options.DB_TYPE
config = stored_options.SQL_LAST_CNX[self.db_type]
if self.db_type == 'sqlite':
db_file_path = config['host']
if not dirname(
db_file_path
): # file_path has not directory, assume it lives in DATA_DIR
db_file_path = join(DATA_DIR, db_file_path)
self.db_name = None
self.cnx = sqlite3.connect(db_file_path)
else:
self.db_name = config['dbname']
self.cnx = psycopg2.connect(**config)
self.cursor = self.cnx.cursor()
self.tables = ['DVHs', 'Plans', 'Rxs', 'Beams', 'DICOM_Files']
def __init__(self):
wx.Dialog.__init__(self, None, title='About DVH Analytics')
scrolled_window = wx.ScrolledWindow(self, wx.ID_ANY)
with open(LICENSE_PATH, 'r') as license_file:
license_text = ''.join([line for line in license_file])
license_text = "DVH Analytics v%s\ndvhanalytics.com\n\n%s" % (Options().VERSION, license_text)
sizer_wrapper = wx.BoxSizer(wx.VERTICAL)
sizer_text = wx.BoxSizer(wx.VERTICAL)
scrolled_window.SetScrollRate(20, 20)
license_text = wx.StaticText(scrolled_window, wx.ID_ANY, license_text)
sizer_text.Add(license_text, 0, wx.EXPAND | wx.ALL, 5)
scrolled_window.SetSizer(sizer_text)
sizer_wrapper.Add(scrolled_window, 1, wx.EXPAND, 0)
self.SetBackgroundColour(wx.WHITE)
self.SetSizer(sizer_wrapper)
self.SetSize((750, 900))
self.Center()
self.ShowModal()
def __init__(self, *config, db_type=None, group=1):
"""
:param config: optional SQL login credentials, stored values used if nothing provided
:param db_type: either 'pgsql' or 'sqlite'
:type db_type: str or None
:param group: use a group-specific connection, either 1 or 2
:type group: int
"""
stored_options = Options()
if config:
self.db_type = db_type if db_type is not None else 'pgsql'
config = config[0]
else:
# Read SQL configuration file
if group == 2 and stored_options.SYNC_SQL_CNX:
group = 1
self.db_type = stored_options.DB_TYPE_GRPS[group] if db_type is None else db_type
config = stored_options.SQL_LAST_CNX_GRPS[group][self.db_type]
if self.db_type == 'sqlite':
db_file_path = config['host']
if not dirname(db_file_path): # file_path has not directory, assume it lives in DATA_DIR
db_file_path = join(DATA_DIR, db_file_path)
self.db_name = None
self.cnx = sqlite3.connect(db_file_path)
else:
self.db_name = config['dbname']
self.cnx = psycopg2.connect(**config)
self.cursor = self.cnx.cursor()
self.tables = ['DVHs', 'Plans', 'Rxs', 'Beams', 'DICOM_Files']
Hierarchy of classes:
Plan -> FxGroup -> Beam -> ControlPoint
"""
# Copyright (c) 2016-2019 Dan Cutright
# This file is part of DVH Analytics, released under a BSD license.
# See the file LICENSE included with this distribution, also
# available at https://github.com/cutright/DVH-Analytics
from dicompylercore import dicomparser
import numpy as np
from shapely.geometry import Polygon
from shapely import speedups
from dvha.tools.utilities import flatten_list_of_lists as flatten
from dvha.options import Options
options = Options()
# Enable shapely calculations using C, as opposed to the C++ default
if speedups.available:
speedups.enable()
class Plan:
"""
Collect plan information from an RT Plan DICOM file.
Automatically parses fraction data with FxGroup class
"""
def __init__(self, rt_plan_file):
"""
:param rt_plan_file: absolute file path of a DICOM RT Plan file
"""
"""
Class to retrieve DVH data from SQL, calculate parameters dependent on DVHs, and extract plotting data
"""
# Copyright (c) 2016-2019 Dan Cutright
# This file is part of DVH Analytics, released under a BSD license.
# See the file LICENSE included with this distribution, also
# available at https://github.com/cutright/DVH-Analytics
from copy import deepcopy
from dateutil.parser import parse as date_parser
import numpy as np
from dvha.db.sql_connector import DVH_SQL
from dvha.db.sql_to_python import QuerySQL
from dvha.options import Options
MAX_DOSE_VOLUME = Options().MAX_DOSE_VOLUME
# This class retrieves DVH data from the SQL database and calculates statistical DVHs (min, max, quartiles)
# It also provides some inspection tools of the retrieved data
class DVH:
def __init__(self, uid=None, dvh_condition=None, dvh_bin_width=5):
"""
This class will retrieve DVHs and other data in the DVH SQL table meeting the given constraints,
it will also parse the DVH_string into python lists and retrieve the associated Rx dose
:param uid: a list of allowed study_instance_uids in data set
:param dvh_condition: a string in SQL syntax applied to a DVH Table query
:param dvh_bin_width: retrieve every nth value from dvh_string in SQL
:type dvh_bin_width: int
"""
def __init__(self, *args, **kwds):
kwds["style"] = kwds.get("style", 0) | wx.DEFAULT_FRAME_STYLE
wx.Frame.__init__(self, *args, **kwds)
self.layout_set = False
self.sizer_dvhs = wx.BoxSizer(wx.VERTICAL)
set_msw_background_color(self) # If windows, change the background color
self.options = Options()
# Initial DVH object and data
self.save_data = {}
self.group_data = {1: {'dvh': None,
'data': {key: None for key in ['Plans', 'Beams', 'Rxs']},
'stats_data': None},
2: {'dvh': None,
'data': {key: None for key in ['Plans', 'Beams', 'Rxs']},
'stats_data': None}}
self.toolbar_keys = ['Open', 'Close', 'Save', 'Export', 'Import', 'Database', 'ROI Map', 'Settings']
self.toolbar_ids = {key: i + 1000 for i, key in enumerate(self.toolbar_keys)}
# sql_columns.py contains dictionaries of all queryable variables along with their
# SQL columns and tables. Numerical categories include their units as well.
self.categorical_columns = sql_columns.categorical
self.numerical_columns = sql_columns.numerical
# Keep track of currently selected row in the query tables
self.selected_index_categorical = None
self.selected_index_numerical = None
# Load ROI Map now and pass to other objects for continuity
# TODO: Need a method to address multiple users editing roi_map at the same time
self.roi_map = DatabaseROIs()
self.query_filters = None
self.reset_query_filters()
self.__add_menubar()
self.__add_tool_bar()
self.__add_layout_objects()
self.__bind_layout_objects()
columns = {'categorical': ['category_1', 'category_2', 'Filter Type'],
'numerical': ['category', 'min', 'max', 'Filter Type']}
self.data_table_categorical = DataTable(self.table_categorical, columns=columns['categorical'])
self.data_table_numerical = DataTable(self.table_numerical, columns=columns['numerical'])
self.__set_properties()
self.__set_tooltips()
self.__add_notebook_frames()
self.__do_layout()
self.disable_query_buttons('categorical')
self.disable_query_buttons('numerical')
self.button_query_execute.Disable()
self.__disable_notebook_tabs()
self.Bind(wx.EVT_CLOSE, self.on_quit)
self.tool_bar_windows = {key: None for key in ['import', 'database', 'roi_map']}
wx.CallAfter(self.__catch_failed_sql_connection_on_app_launch)
self.__do_subscribe()