transphire package (Developer area)¶
Subpackages¶
Submodules¶
transphire.buttoncontainer module¶
transphire.emaildialog module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
transphire.framecontainer module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.framecontainer.
FrameContainer
(parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
FrameContainer widget.
Inherits from: QWidget
Buttons: Add - Add FrameWidget widget to the layout
LineEdit: First frame - First frame to use for a smaller amount of dose Last frame - Last frame to use for a smaller amount of dose
-
add_widget
()[source]¶ Add a FrameWidget widget to the dynamic layout. Called when the add button is clicked.
Arguments: None
Returns: None
-
enable
(var, use_all)[source]¶ Enable or disable the buttons and widgets.
Arguments: var - State of buttons (True or False) use_all - Disable all buttons (True) or only some (False)
Return: None
-
transphire.framewidget module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.framewidget.
FrameWidget
(first, last, dose_weight, default, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
FrameWidget widget.
Inherits from: QWidget
Buttons: Delete - Delete this instance of the variable.
Signals: delete - Delete this instance of the variable (class instance).
-
delete
¶
-
transphire.inputbox module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.inputbox.
InputBox
(is_password, restart_names=None, is_stop=False, settings=None, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QDialog
Show a message box with an input field.
Inherits: QDialog
Signals: None
-
setDefault
(text)[source]¶ Set the default values for the QLineEdit.
text - Text to put
Returns: None
-
transphire.loadcontent module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.loadcontent.
LoadContent
(typ, separator, settings_folder, hdd=None, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
LoadContent widget. Widget used for the LoadContentContainer.
Inherits from: QWidget
Signals: delete - Emited, when the delete button is pressed (object)
-
delete
¶
-
transphire.loadcontentcontainer module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.loadcontentcontainer.
LoadContentContainer
(typ, template_name, templates, settings_folder, is_shared, default_file, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
LoadContentContainer widget Inherits from: QWidget
Buttons: Save settings - Save currently defined settings to settings files Add - Add new Mount entry (Case Mount)
-
add_widget
(name=None, hdd=None)[source]¶ Add new widget to layout.
Arguments: name - Name of new mount point (default None) hdd - Is hdd entry (default None)
Return: None
-
get_settings
()[source]¶ Get settings from tab or normal normal widget.
Arguments: None
Return: List of widget settings
-
get_settings_tab
()[source]¶ Get settings from tab widget.
Arguments: None
Return: List of widget settings
-
get_settings_widget
()[source]¶ Get settings from normal widget.
Arguments: None
Return: List of widget settings
-
remove_widget
(separator)[source]¶ Remove widget from layout.
Arguments: separator - List of seperator widgets
Return: None
-
transphire.loadwindow module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.loadwindow.
DefaultSettings
(apply, settings_directory, template_name, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QDialog
DefaultSettings dialog. Dialog used to enter default values.
Inherits from: QDialog
-
accept_apply
()[source]¶ Set the apply settings variable to True before saving.
Argumens: None
Return: None
-
add_tab
(widget, name)[source]¶ Add a new widget to the tab widget
Arguments: widget - Widget to add as new tab Name - Name of the new tab
Return: None
-
check_modified_widgets
(done)[source]¶ Check, if a widget is modified before saving.
Arguments: done - If True, close after input, else apply settings.
Return: True if no modification, else False
-
fill_default_dict
()[source]¶ Fill the default dict with the information from the function dict.
Arguments: None - The self.default_dict is used
Returns: None - The self.default_dict is changed in-place
-
get_apply
()[source]¶ Getter for the self.apply variable.
Arguments: None
Return: Content of self.apply
-
static
get_content_default
(edit_settings, apply, settings_folder, template_name)[source]¶ Staticmethod to open the default content dialog.
Arguments: edit_settings - If True, open default settings dialog, else just return content apply - Apply settings after closing the default settings dialog settings_folder - Folder to store the default settings
Return: Content for the widgets, Content of the apply variable
-
transphire.logviewer module¶
transphire.logviewerdialog module¶
transphire.mainwindow module¶
transphire.messagebox module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
transphire.mountcalculator module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.mountcalculator.
MountCalculator
(name, parent=None)[source]¶ Bases:
PyQt5.QtCore.QObject
MountCalculator object.
Inherits from: QObject
Buttons: None
Signals: sig_finished - Signal emitted, if process finished (str, str, str)
-
calculate_df_quota
(key, mount_folder)[source]¶ Calculate the quota with the help of the df command.
Arguments: key - Mount point key mount_folder - Mount folder
Return: None
-
calculate_get_quota
(key, quota, mount_folder)[source]¶ Calculate the quota by calculating the size of every file.
Arguments: key - Mount point key mount_folder - Mount folder quota - User provided maximum quota
Return: None
-
calculate_ssh_quota
(user, folder, device, mount_folder, ssh_dict, quota_command_dict, password_dict)[source]¶ Calculate the quota via ssh.
Arguments: mount_folder - Mount folder user - Username folder - Folder to mount device - Device name ssh_dict - ssh_dict containing ssh information quota_command_dict - Dictionary containing the quota commands password_dict - Dictionary containing passwords
Return: None
-
get_folder_size
(folder, size)[source]¶ Get the size of the folder recursively
Arguments: folder - Folder to check contents size - Current caclulated size
Return: Calculated size
-
static
get_quota_quota_command
(text, folder)[source]¶ Extract the quota from the quota command.
Arguments: text - Text returned by quota command. folder - Mounted folder
Return: None
-
get_ssh_quota
(user, folder, device)[source]¶ Get the quota via ssh command.
Arguments: user - User name folder - Mounted folder device - Device name
Return: None
-
sig_finished
¶
-
transphire.mountcontainer module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.mountcontainer.
MountContainer
(content_mount, mount_worker, parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
MountContainer widget.
Inherits from: QWidget
Buttons: None
Signals: None
transphire.mountwidget module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.mountwidget.
MountWidget
(content, mount_worker, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
MountWidget widget.
Inherits from: QWidget
Buttons: mount_button - Mount mount point umount_button - Umount mount point
Signals: None
-
get_settings
()[source]¶ Return settings of the content.
Arguments: None
Returns: Settings as dictionary
-
transphire.mountworker module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.mountworker.
MountWorker
(password, settings_folder, mount_directory, parent=None)[source]¶ Bases:
PyQt5.QtCore.QObject
Mounting and unmounting shared devices.
Inherits from: QObject
Buttons: None
Signals: sig_mount_hdd - Signal connected to mount HDD (device|str) sig_mount - Signal connected to mount a mount point (device|str, user|str, password|str, folder|str, server|str, typ|str, domain|str, version|str, sec|str, gid|str) sig_umount - Signal connected to unmount a mount point (device_folder|str, device|str, thread|object)
sig_success - Signal emitted, if a task was a success (text|str, device|str, color|str) sig_error - Signal emitted, if a task was a failure (text|str, device|str) sig_info - Signal emitted, to show text in a text box (text|str) sig_notification - Signal emitted, to send a notification message (text|str)
sig_add_save - Signal connected to add a save file to the dictionary (device|str, ss_address|str, quota_command|str, is_right_quota|str, quota|str) sig_load_save - Signal connected to load data from save file (No object) sig_refresh - Signal connected to recalculate quota (No object) sig_quota - Signal emitted, to refresh the quota status in the GUI (text|str, device|str, color|str) sig_set_settings - Signal connected set quota related settings (settings|object)
sig_calculate_ssh_quota - Signal emitted to calculate the quota via ssh (user|str, folder|str, device|str, mount_folder|str, ssh_dict|object, quota_command_dict|object, password_dict|object) sig_calculate_df_quota - Signal emitted to calculate the quota via system information (device|str, mount_folder|str) sig_calculate_get_quota - Signal emitted to calculate the quota brute force (device|str, total_quota|str, mount_folder|str)
-
add_save
(device, ssh_address, quota_command, is_right_quota, quota)[source]¶ Add a save file to the dictonaries.
Arguments: device - Mounted device name ssh_address - ssh adress quota_command - Command to calculate quota via ssh is_right_quota - True, if df is showing the right quota quota - Provided maximum quota
Return: None
-
fill_quota_project_and_scratch
(name, directory, warning, quota_limit)[source]¶ Refresh quota information for the project and scratch directory.
Arguments: name - Name (project or scratch) directory - Directory to check warning - current warning status quota_limit - Limit of the quota to show a warning
Return: Current warning status
-
mount
(device, user, password, folder, server, typ, domain, version, sec, gid, folder_from_root, fixed_folder)[source]¶ Mount device except HDD
Arguments: device - Device name user - Username password - User password folder - Mount folder server - Server name typ - Mount type domain - Domain name version - Mount type version sec - security protocol gid - groupid to mount folder_from_root - Absolute path pointing towards the mount point
Return: None
-
set_settings
(settings)[source]¶ Set settings used by the worker.
Arguments: settings - TranSPHIRE settings
Return: None
-
sig_add_save
¶
-
sig_calculate_df_quota
¶
-
sig_calculate_get_quota
¶
-
sig_calculate_ssh_quota
¶
-
sig_error
¶
-
sig_info
¶
-
sig_load_save
¶
-
sig_mount
¶
-
sig_mount_hdd
¶
-
sig_notification
¶
-
sig_quota
¶
-
sig_refresh
¶
-
sig_set_folder
¶
-
sig_set_settings
¶
-
sig_success
¶
-
sig_umount
¶
-
transphire.notificationcontainer module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.notificationcontainer.
NotificationContainer
(content, mount_worker, process_worker, settings_folder, parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
Container for notification widgets
Inherits: QWidget
Signals: sig_stop - Signal is emitted, if the user is sending /stop via telegram
-
enable
(var, use_all)[source]¶ Enable or disable the widgets of the widget.
Arguments: var - True(Enable) or False(Disable) use_all - Disable or enable all
Returns: None
-
get_telegram_messages
()[source]¶ Check the messages in telegram for commands.
Arguments: None
Returns: None
-
get_telegram_user
(page)[source]¶ Get the users and the user id
Arguments: page - Webpage of the telegram bot
Returns: Dictionary of users
-
send_notification
(text)[source]¶ Send a notification to specified users.
Arguments: text - Text to send
Returns: None
-
send_to_user
(user_id, text, name)[source]¶ Send a message to all users.
Arguments: user_id - User id of the receiving person text - Text of the message name - Name of the sender
Returns: None
-
set_settings
(settings)[source]¶ Set settings.
Arguments: settings - Settings as dictionary to set.
Returns: None
-
sig_stop
¶
-
transphire.notificationwidget module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.notificationwidget.
NotificationWidget
(name, default, default_programs_dict, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
Widget for notification phone numbers
-
add_exceptions
(name)[source]¶ Add a person to the exception list and dont send notification anymore.
Arguments: name - Name of the person
Returns: None
-
get_settings
()[source]¶ Get text of the currently selected combo item.
Arguments: None
Returns: Settings dictionary
-
transphire.passworddialog module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
transphire.plotcontainer module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.plotcontainer.
PlotContainer
(name, content, plot_labels, plot_name, plot_worker, plot_type, layout, *args, parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QMainWindow
Qwidget in combination with a FigureCanvas.
Inherits: QMainWindow
-
activate_tab
(name)[source]¶ Activate the tab with the name: name.
Arguments: name - Name of the activation
Returns: None
-
enable
(var, use_all)[source]¶ Enable or disable the widgets.
var - It True, enable widgets, else disable use_all - If True, enable/disable all widgets, else only a subset
Returns: None
-
transphire.plotwidget module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.plotwidget.
MplCanvas
(no_grid, width=5, height=5, dpi=100, parent=None)[source]¶ Bases:
matplotlib.backends.backend_qt5agg.FigureCanvasQTAgg
-
sig_twin
¶
-
-
class
transphire.plotwidget.
MplCanvasWidget
(no_grid, plot_type, is_twin=False, width=5, height=5, dpi=100, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
-
class
transphire.plotwidget.
PlotWidget
(label, plot_typ, dock_widget, twin_container, *args, parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
PlotWidget widget. Widget used to show data plots.
Inherits from: QWidget
Signals: None
-
class
transphire.plotwidget.
SelectWidget
(parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
-
sig_update
¶
-
transphire.plotworker module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.plotworker.
PlotWorker
(parent=None)[source]¶ Bases:
PyQt5.QtCore.QObject
Plot different information about motion correction and ctf estimation.
Inherits: QObject
Signals: sig_data - Emitted, if data for plotting is found (name|str, data|object, directory|str, settings|object) sig_notification - Emitted, if phase plate limit is reached. (text|str)
-
set_settings
(settings)[source]¶ Set settings for the calculation of the arrays.
name - Name of the software that calls the calculation directory_name - Name of the directory that contains the log files settings - TranSPHIRE settings
Returns: None
-
sig_calculate
¶
-
sig_data
¶
-
sig_new_round
¶
-
sig_reset
¶
-
sig_reset_list
¶
-
sig_set_visual
¶
-
sig_visible
¶
-
transphire.processthread module¶
transphire.processworker module¶
transphire.separator module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
transphire.settingscontainer module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.settingscontainer.
SettingsContainer
(content, name, global_dict, settings_folder, mount_worker, parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
Widget for setting widgets.
Inherits: QWidget
-
change_state
(name)[source]¶ Change the state of widgets based on the choice of the corresponding combo box
name - Name of the group to change status (Emitted by the combo box)
Returns: None
-
enable
(var, use_all)[source]¶ Disable or enable all widgets
Arguments: var - If True, enable the widgets, else disable them use_all - If True, all widgets are enabled/disabled
Returns: None
-
get_settings
(quiet=False)[source]¶ Get the settings as dict
Arguments: quiet - If True, no prints are executed
Returns: Settings as dictionary
-
set_design
(settings)[source]¶ Set settings to the widgets
Arguments: settings - Settings to set.
Returns: None
-
set_settings
(settings)[source]¶ Set settings to the widgets
Arguments: settings - Settings to set.
Returns: None
-
sig_adjust_tab
¶
-
sig_change_use_movie
¶
-
transphire.settingswidget module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.settingswidget.
SettingsWidget
(name, content, content_others, mount_directory, global_dict=None, input_file_names=None, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
Widget for setting entrys
Inherits: QWidget
Signals: sig_index_changed - Emitted, if the index of a combo box changes (Combo box name|str)
-
change_color_if_true
()[source]¶ Change the color, if the types are all true.
Arguments: None
Returns: None
-
get_combo_entries
()[source]¶ Get the entries of the combo boxes.
Arguments: None
Returns: List containing entries.
-
get_settings
(quiet=False)[source]¶ Get the settings as dict.
Arguments: quiet - True, if prints should not be shown.
Returns: None, if an error occured. Settings as dictionary.
-
set_settings
(text, is_checked)[source]¶ Set settings
text - Text to set to the widget.
Returns: None
-
sig_index_changed
¶
-
transphire.statuscontainer module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.statuscontainer.
StatusContainer
(content, content_mount, content_pipeline, mount_worker, process_worker, content_font, parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
Container for status widgets
Inherits: QWidget
Signals: sig_refresh_quota - Connected to change the quota text (no object)
-
refresh_quota
(text, device, color)[source]¶ Refresh the quota
Arguments: text - Text to show device - Device name color - Color of the text
Returns: None
-
sig_refresh_quota
¶
-
transphire.statuswidget module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.statuswidget.
StatusWidget
(name, default_name, default_quota, parent=None)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
Widget to show the current status of the processes.
Inherits: QWidget
Signals: sig_change_info_name - Connected, to change the info name information (text|str, color|str) sig_change_info_quota - Connected, to change the quota name information (text|str, color|str)
-
change_info_name
(text, color)[source]¶ Change the info text and the info text color.
Arguments: text - Text to put color - Color to use
Returns: None
-
change_info_quota
(text, color)[source]¶ Change the info text and the info text color.
Arguments: text - Text to put color - Color to use
Returns: None
-
sig_change_info_name
¶
-
sig_change_info_quota
¶
-
transphire.tabdocker module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
class
transphire.tabdocker.
TabDocker
(parent=None, **kwargs)[source]¶ Bases:
PyQt5.QtWidgets.QWidget
Tab widget for the settingswidgets.
Inherits: QWidget
-
add_tab
(widget, name, add_widgets=True)[source]¶ Add a new tab to the TabDocker
Arguments: widget - Widget to add name - Name of the widget
Return: None
-
currentIndex
()[source]¶ Get the current Index of the tab_widget.
Returns: Current index of self.tab_widget
-
enable_tab
(visible)[source]¶ Enable or disable the tab.
Arguments: visible - Enable if True, Disable if False name - Name of the tab to disable.
Returns: None
-
indexOf
(widget)[source]¶ Get the index of the widget.
Arguments: widget - Adress of the widget
Returns: Index of the widget
-
latest_active
= [None]¶
-
removeTab
(idx)[source]¶ Remove the widget located at tab idx
Arguments: idx - Idx of the widget
Returns: None
-
setCurrentIndex
(idx)[source]¶ Set the current Index of the tab_widget.
Arguments: idx - Index to set
Returns: Current index of self.tab_widget
-
setCurrentWidget
(widget)[source]¶ Set the current widget of the tab_widget.
Arguments: idx - Widget to set
Returns: Current index of self.tab_widget
-
setMovable
(status)[source]¶ Set the movable status for the tab widgets
Arguments: status - Boolean variable for the status
Returns: None
-
setTabEnabled
(index, state)[source]¶ Set the tab position index to the enable state.
Arguments: index - Tab position index state - State (True or False)
Returns: None
-
setTabPosition
(position)[source]¶ Set the tab position of the Tab bar
Arguments: position - Tab position as string [‘North’, ‘East’, ‘West’, ‘South’]
Returns: None
-
setTabText
(idx, text)[source]¶ Set the text for the tab at idx
Arguments: idx - Index of the tab text - Text of the tab
Returns: None
-
sig_start_plot
¶
-
transphire.templatedialog module¶
transphire.transphire_class2d module¶
transphire.transphire_content module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
transphire.transphire_content.
default_auto_sphire_v1_3
()[source]¶ Content for auto sphire
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cinderella_v0_3_1
()[source]¶ Content of cinderella v0.3.1
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_compress_command_line
()[source]¶ Content for compression
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_copy
(settings_folder)[source]¶ Content of Copy tab.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_train_v1_5_4
()[source]¶ Content of crYOLO_train version 1.5.4
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_train_v1_5_8
()[source]¶ Content of crYOLO_train version 1.5.8
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_train_v1_7_4
()[source]¶ Content of crYOLO_train version 1.7.4
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_v1_0_4
()[source]¶ Content of crYOLO version 1.0.4
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_v1_1_0
()[source]¶ Content of crYOLO version 1.1.0
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_v1_2_1
()[source]¶ Content of crYOLO version 1.2.1
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_v1_4_1
()[source]¶ Content of crYOLO version 1.4.1
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cryolo_v1_5_8
()[source]¶ Content of crYOLO version 1.5.8
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_cter_v1_0
()[source]¶ Content of CTER SPHIRE version 1.0.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_ctffind_4_v4_1_8
()[source]¶ Content of CTFFind version 4.1.8.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_font
()[source]¶ Content of Font tab.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_gctf_v1_06
()[source]¶ Content of GCtf version 1.06.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_gctf_v1_18
()[source]¶ Content of GCtf version 1.18.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_general
()[source]¶ Content of General tab.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_input
()[source]¶ Content of General tab.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_isac2_1_2
()[source]¶ Content of sp_isac2(gpu) version 1.2
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_motion_cor_2_v1_0_0
()[source]¶ Content of MotionCor2 version 1.0.0.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_motion_cor_2_v1_0_5
()[source]¶ Content of MotionCor2 version 1.0.5.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_motion_cor_2_v1_1_0
()[source]¶ Content of MotionCor2 version 1.1.0.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_motion_cor_2_v1_3_0
()[source]¶ Content of MotionCor2 version 1.3.0.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_mount
(hdd=None)[source]¶ Content of Mount tab.
Arguments: hdd - Content is related to HDD
Return: Content items as list
-
transphire.transphire_content.
default_notification
()[source]¶ Content of notification tab.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_notification_widget
()[source]¶ Content of notification widget.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_others
(settings_folder)[source]¶ Content of Status tab.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_path
()[source]¶ Content of Path tab.
Arguments: None
Return: Content items as list
-
transphire.transphire_content.
default_pipeline
()[source]¶ Content of pipeline tab.
Arguments: None
Return: Content items as list
transphire.transphire_ctf module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
transphire.transphire_ctf.
combine_ctf_outputs
(data, data_orig, root_path, file_name, settings, queue_com, shared_dict, name, sum_file, dw_file)[source]¶ Combine the ctf outputs to one SPHIRE partres and one RELION star file.
root_path - Root path of the file file_name - File name of the ctf file. settings - TranSPHIRE settings queue_com - Queue for communication name - Name of process sum_file - Name of the dose uncorrected sum file
Returns: None
-
transphire.transphire_ctf.
contrast_to_shift
(a_cont)[source]¶ Transform amplitude contrast to phase shift.
a_cont - Amplitude contrast value in percent
Returns: Phase shift in degrees.
-
transphire.transphire_ctf.
create_cter_1_0_command
(ctf_name, file_sum, file_input, output_dir, settings)[source]¶ Create the CTER v1.0 command
-
transphire.transphire_ctf.
create_cter_1_3_command
(ctf_name, file_sum, file_input, output_dir, settings)[source]¶ Create the CTER v1.3 command
-
transphire.transphire_ctf.
create_ctffind_4_v4_1_13_command
(ctf_name, file_sum, file_input, file_output, set_name, settings)[source]¶ Create the ctffind command
-
transphire.transphire_ctf.
create_ctffind_4_v4_1_8_command
(ctf_name, file_sum, file_input, file_output, set_name, settings)[source]¶ Create the ctffind command
-
transphire.transphire_ctf.
create_export_data
(export_data, lines, maximum_string)[source]¶ Write export data to file.
export_data - Data to export. file_name - Name of the file to write to.
Returns: In place modificaion of lines
-
transphire.transphire_ctf.
create_gctf_v1_06_command
(ctf_name, file_sum, file_input, file_output, settings, name)[source]¶ Create the Gctf v1.06 command
-
transphire.transphire_ctf.
find_logfiles
(root_path, file_name, settings, queue_com, name)[source]¶ Find logfiles related to the produced CTF files.
root_path - Root path of the file file_name - File name of the ctf file. settings - TranSPHIRE settings queue_com - Queue for communication name - Name of process
Returns: list of log files
-
transphire.transphire_ctf.
get_constant_value
(key, ctf_settings, row, project_folder, ctf_name, ctf_folder, pixel_size_adjust)[source]¶
-
transphire.transphire_ctf.
get_ctf_command
(file_sum, file_input, new_name, settings, queue_com, set_name, name)[source]¶ Create the ctf command based on the ctf software.
file_input - Input name of the file for ctf estimation new_name - Output file settings - TranSPHIRE settings queue_com - Queue for communication name - Name of process
Returns: CTF command File to check vor validation if the process was successful
-
transphire.transphire_ctf.
get_relion_header
(names)[source]¶ Create a relion star file header.
names - Header names as list
Returns: header string
-
transphire.transphire_ctf.
recursive_file_search
(directory, files)[source]¶ Recursive file search function.
-
transphire.transphire_ctf.
shift_to_contrast
(phase_shift)[source]¶ Convert phase shift to amplitud contrast.
phase_shift - Phase shift in degrees.
Returns: Amplitude contrast in percent.
-
transphire.transphire_ctf.
to_partres_file
(data, ctf_name, ctf_settings, project_folder, ctf_folder, sum_file, pixel_size_adjust)[source]¶ Create a CTF partres file from data
data - Array containing ctf information. ctf_name - Name of the ctf program. ctf_settings - Settings for this ctf estimation run. project_folder - Name of the project folder. ctf_folder - Name of the ctf output folder. sum_file - Name of the summed micrograph image
Returns: None
-
transphire.transphire_ctf.
to_star_file
(data, ctf_name, ctf_settings, project_folder, ctf_folder, sum_file, dw_file, pixel_size_adjust)[source]¶ Create a CTF star file from data
data - Array containing ctf information. ctf_name - Name of the ctf program. ctf_settings - Settings for this ctf estimation run. project_folder - Name of the project folder. ctf_folder - Name of the ctf output folder. sum_file - Name of the sum file
Returns: None
transphire.transphire_extract module¶
transphire.transphire_import module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
transphire.transphire_import.
dummy
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶
-
transphire.transphire_import.
get_dtype_dict
()[source]¶ Dtype of the data plot array.
Arguments: None
Return: Dtype dict
-
transphire.transphire_import.
get_dtype_import_dict
()[source]¶ Dtype of the file to import.
Arguments: None
Return: Dtype dict
-
transphire.transphire_import.
get_header
(input_file)[source]¶ Extract header information from a relion star file.
Arguments: input_file - Input star file
Return: Color string
-
transphire.transphire_import.
get_relion_dict
()[source]¶ Translate relion star file information to dtype dict.
Arguments: None
Return: Dtype dict
-
transphire.transphire_import.
get_transphire_dict
()[source]¶ Translate transphire ctf dict into relion star file information.
Arguments: None
Return: Dtype dict
-
transphire.transphire_import.
import_auto_sphire_v1_3
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶ Import motion information for auto_sphire.py version 1.3
Arguments: name - Name of motion program directory_name - Name of the directory to search for files
Return: Imported data
-
transphire.transphire_import.
import_cinderella_v0_3_1
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶
-
transphire.transphire_import.
import_cryolo_v1_0_4
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None, sub_directory=None)[source]¶ Import picking information for crYOLO v1.0.4.
Arguments: name - Name of picking program directory_name - Name of the directory to search for files
Return: Imported data
-
transphire.transphire_import.
import_cryolo_v1_2_2
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶ Import picking information for crYOLO v1.2.2.
Arguments: name - Name of picking program directory_name - Name of the directory to search for files
Return: Imported data
-
transphire.transphire_import.
import_cter_v1_0
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶ Import ctf information for CTER v1.0. Defocus in angstrom, phase shift in degree.
Arguments: name - Name of ctf program directory_name - Name of the directory to search for files
Return: Imported data
-
transphire.transphire_import.
import_ctffind_v4_1_8
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶ Import ctf information for CTFFIND v4.1.8. Defocus in angstrom, phase shift in degree.
Arguments: name - Name of ctf program directory_name - Name of the directory to search for files
Return: Imported data
-
transphire.transphire_import.
import_gctf_v1_06
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶ Import ctf information for Gctf v1.06. Defocus in angstrom, phase shift in degree.
Arguments: name - Name of ctf program directory_name - Name of the directory to search for files
Return: Imported data
-
transphire.transphire_import.
import_isac_v1_2
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶
-
transphire.transphire_import.
import_motion_cor_2_v1_0_0
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶ Import motion information for MotionCor2 v1.0.0.
Arguments: name - Name of motion program directory_name - Name of the directory to search for files
Return: Imported data
-
transphire.transphire_import.
import_unblur_v1_0_0
(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]¶ Import motion information for cisTEM Unblur v1.0.0.
Arguments: name - Name of motion program directory_name - Name of the directory to search for files
Return: Imported data
transphire.transphire_motion module¶
transphire.transphire_picking module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
transphire.transphire_picking.
create_circle
(jpg_data, maskcenters, radius)[source]¶ Create a circle in a numpy array
Arguments: jpg_data - Data that needs to be changed maskcenters - center of mask radius - Radius of the circle
Returns: None, jpg_data will be changed in-place
-
transphire.transphire_picking.
create_cryolo_v1_0_4_command
(picking_name, file_input, file_output, settings, name)[source]¶ Create the crYOLO v1.0.4 command
-
transphire.transphire_picking.
create_cryolo_v1_1_0_command
(picking_name, file_input, file_output, settings, name)[source]¶ Create the crYOLO v1.1.0 command
-
transphire.transphire_picking.
create_cryolo_v1_4_1_command
(picking_name, file_input, file_output, settings, name)[source]¶ Create the crYOLO v1.1.0 command
-
transphire.transphire_picking.
find_logfiles
(root_path, file_name, settings, queue_com, name)[source]¶ Find logfiles related to the produced CTF files.
root_path - Root path of the file file_name - File name of the ctf file. settings - TranSPHIRE settings queue_com - Queue for communication name - Name of process
Returns: list of log files
-
transphire.transphire_picking.
get_picking_command
(file_input, new_name, settings, queue_com, name)[source]¶ Create the picking command based on the picking software.
file_input - Input name of the file for ctf estimation new_name - Output file settings - TranSPHIRE settings queue_com - Queue for communication name - Name of process
Returns: Picking command File to check vor validation if the process was successful
transphire.transphire_plot module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
transphire.transphire_plot.
get_mic_number
(array, settings, as_int=True)[source]¶ Identify the micrograph number out of the name string.
Arguments: array - Array containing information settings - User provided settings
Return: Array of micrograph numbers
-
transphire.transphire_plot.
update_batch
(data, settings, label)[source]¶ Update the plot for crYOLO v1.0.4.
Arguments: data - Data to plot settings - User provided settings label - Label of the plot
Return: x values, y values, label, title
-
transphire.transphire_plot.
update_cryolo_v1_0_4
(data, settings, label)[source]¶ Update the plot for crYOLO v1.0.4.
Arguments: data - Data to plot settings - User provided settings label - Label of the plot
Return: x values, y values, label, title
-
transphire.transphire_plot.
update_ctf
(data, settings, label)[source]¶ Update the plot for CTFFIND v4.1.8.
Arguments: data - Data to plot settings - User provided settings label - Label of the plot
Return: x values, y values, label, title
transphire.transphire_select2d module¶
transphire.transphire_software module¶
transphire.transphire_train2d module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
transphire.transphire_train2d.
create_eval_command
(config_file, weight_file, log_file, settings, name)[source]¶
transphire.transphire_utils module¶
TranSPHIRE is supposed to help with the cryo-EM data collection Copyright (C) 2017 Markus Stabrin
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
-
transphire.transphire_utils.
check_instance
(value, typ)[source]¶ Check typ of value
Arguments: value - Value to check typ - Type to check
Return: Bool
-
transphire.transphire_utils.
copy
(file_in, file_out)[source]¶ Copy file_in to a new location.
Arguments: file_in - Input file file_out - Output file
Return: None
-
transphire.transphire_utils.
create_log
(*args)[source]¶ Add a time string to print statement.
args - Args to print
Returns: String with added time stemp.
-
transphire.transphire_utils.
find_best_match
(name, dictionary)[source]¶ Find the best matching version key in a dictionary. Raises an assertion error it the return_key is not valid.
name - Name of the current version. dictionary - Dictionary to find the best matching version.
Returns: The best matching version Key.
-
transphire.transphire_utils.
find_latest_version
(name, dictionary)[source]¶ Find the latest matching version key in a dictionary. Raises an assertion error it the return_key is not valid.
name - Name of the program dictionary - Dictionary to find the best matching version.
Returns: The best matching version Key.
-
transphire.transphire_utils.
get_color
(typ)[source]¶ Color defined for the type
Arguments: typ - Typ of color
Return: Color string
-
transphire.transphire_utils.
get_content_gui
(content, template_name, n_feedbacks)[source]¶ Create content lists to load the GUI.
Arguments: content - Content as dictionary. template_name = Name of the template!
Return: Content as list
-
transphire.transphire_utils.
get_exclude_set_path
(content)[source]¶ Check the widget_2 variable, if the program should be loaded or not.
Argument: content - Content as dictionary.
Return: List of names to exclude
-
transphire.transphire_utils.
get_function_dict
()[source]¶ Return a dictionary containing the function to use for specific plots.
Arguments: None
Return: None
-
transphire.transphire_utils.
get_key_names
(settings_folder, name)[source]¶ Extract mount names from related settings file.
Arguments: None
Return: List of mount names
-
transphire.transphire_utils.
get_name
(name)[source]¶ Remove the extension of a file and return the basename without the PATH
name - Name to remove the extension from
Returns: The name of the file without PATH and extension.
-
transphire.transphire_utils.
get_style
(typ)[source]¶ Style colores for the content of widgets.
Arguments: typ - Typ of color
Return: Color string
-
transphire.transphire_utils.
is_higher_version
(name, version_ref)[source]¶ Compare the versions of software. The versions do not need to match in digits. v1 > v0, v0.0, v0.0.0 v1 >= v1 v1 < v1.0.1
name - Name of the Software containing the version string, e.g. v1, v1.1, v1.1.1, v1.1.1rc2 version_ref - reference version as string, e.g. 1, 1.1, 1.1.1
Returns: True if the version is larger than the reference version
-
transphire.transphire_utils.
look_and_feel
(app, font=None, adjust_width=None, adjust_height=None, default=None)[source]¶ Look and feel.
Arguments: app - QApplication. font - User provided font size (default None) adjust_width - User provided width adjustment (default None) adjust_height - User provided height adjustment (default None) default - Default values (default None)
Return: Style sheet
-
transphire.transphire_utils.
look_and_feel_small
(app, font=None)[source]¶ Look and feel for the default settings dialog.
Arguments: app - QApplication. font - User provided font size (default None)
Return: Style sheet
-
transphire.transphire_utils.
message
(text)[source]¶ Show a text in a message box.
Arguments: text - Text shown in the message box
Return: None
-
transphire.transphire_utils.
mkdir_p
(path)[source]¶ Create output directories recursively.
Arguments: path - Directory path to create
Return: None
-
transphire.transphire_utils.
question
(head, text)[source]¶ Show a questions message box dialog.
Arguments: head - Header of the window text - Text with the questions
Return: True if No, False if Yes
-
transphire.transphire_utils.
reduce_copy_entries
(exclude_set, content)[source]¶ Reduce the number of options based on the exclude_set
Arguments: exclude_set - Set of names to not consider content - Content of the widgets
Return: None
-
transphire.transphire_utils.
reduce_path_widget
(exclude_set, content)[source]¶ Reduce the number of paths based on the exclude_set
Arguments: exclude_set - Set of names to not consider content - Content of the widgets
Return: None
-
transphire.transphire_utils.
reduce_programs
(exclude_set=None)[source]¶ Reduce the number of programs to the users preferences.
Arguments: exclude_set - Set of names to not consider
Return: List of content for motion, List of content for ctf