transphire package (Developer area)

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/>.

class transphire.emaildialog.EmailDialog(parent=None)[source]

Bases: PyQt5.QtWidgets.QDialog

EmailDialog widget.

Inherits from: QDialog

Buttons: OK Cancel

LineEdit: Name - Name, that associates with the E-Mail E-Mail - E-Mail adress of the user

get_email()[source]

Return the text of the E-Mail.

Arguments: None

Return: E-Mail

get_name()[source]

Return the text of the Name.

Arguments: None

Return: Name

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

get_settings()[source]

Get settings of all FrameWidget widgets.

Arguments: None

Returns: settings - List of FrameWidget settings

set_settings(settings)[source]

Add FrameWidget widgets to the dynamic layout based on setting entries.

Arguments: settings - List of FrameWidget settings.

Returns: 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
get_settings()[source]

Get the settings

Arguments: None

Return: settings as dictionary

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

getText()[source]

Get the text from the label.

Arguments: None

Returns: Text content

get_restart_dict()[source]
handle_check(state)[source]
setDefault(text)[source]

Set the default values for the QLineEdit.

text - Text to put

Returns: None

setText(heading, text)[source]

Set the text to the label.

Arguments: heading - Heading of the window text - Text of the label

Returns: None

set_type(this_type)[source]

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
get_settings()[source]

Get the settings from the child widgets.

Arguments: None

Return: List of settings

set_settings(settings)[source]

Set settings to the entry widgets.

Arguments: settings - List of settings

Return: None

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

copy_from_template(template)[source]
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

save_settings()[source]

Save settings specified in widget to json text file.

Arguments: None

Return: None

set_settings(settings)[source]

Set settings to widget.

Arguments: settings - List of widget settings

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

add_tabs()[source]
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

clear_tabs()[source]
closeEvent(event)[source]

Handle the close event.

Arguments: event - Close event

Return: None

create_initial_tabs(tab_dict, parent_widget, is_old=False)[source]
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

is_in_content(tab_dict, name)[source]
load_template()[source]
recursive_clear(tab_widget)[source]

transphire.logviewer module

class transphire.logviewer.LogViewer(show_indicators=False, indicator='', file_name='', parent=None)[source]

Bases: PyQt5.QtWidgets.QWidget

appendPlainText(text, indicator='log', user=False)[source]
change_state(state)[source]
get_indicator(indicator)[source]
increment_indicator(indicator, text='')[source]
my_click_event(event=None)[source]
reset_plain_text(text)[source]
set_project_path(project_path, log_path, error_path)[source]
submit_text()[source]
update_plain_text(force=False)[source]

transphire.logviewerdialog module

class transphire.logviewerdialog.LogViewerDialog(parent=None)[source]

Bases: PyQt5.QtWidgets.QDialog

add_tab(widget, name)[source]

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/>.

class transphire.messagebox.MessageBox(is_question, parent=None)[source]

Bases: PyQt5.QtWidgets.QDialog

Show a message box

Inherits: QDialog

Signals: None

setDefault(text)[source]
setText(heading, text)[source]

Set the text to the label.

Arguments: heading - Heading of the window text - Text of the label

Returns: None

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

enable(var, use_all)[source]

Enable or disable the content.

Arguments: var - State of buttons (True or False) use_all - Disable all buttons (True) or only some (False)

Return: None

get_settings()[source]

Return settings of the container.

Arguments: None

Return: Settings as list

set_threadlist(thread_list)[source]

Set the thread instances for the different objects.

Arguments: thread_list - List of mount threads

Return: 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

mount()[source]

Mount device preparation

Arguments: None

Return: None

set_current_folder(device, folder)[source]
set_thread_object(thread_object)[source]

Set the thread object.

thread_object - Thread object to set.

Returns: None

umount()[source]

Umount device signal preparation

Arguments: None

Return: None

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

check_connection()[source]

Check if a mount connection crashed

Arguments: None

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

load_save()[source]

Load connection status from the files

Arguments: None

Return: None

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

mount_hdd(device)[source]

Mount external HDD

Arguments: device - Device name

Return: None

refresh_quota()[source]

Refresh quota information.

Arguments: None

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
umount(device_folder, device, fixed_folder, thread_object)[source]

Unmount device

Arguments: device_folder - Mount point folder device - Device name thread_object - Thread object that is connected to the mount point

Return: None

transphire.mountworker.check_existence(mount_directory, mount_folder)[source]

Check existence of the mount folder and create it if it does not

Arguments: mount_folder - tolder to check

Return: True, if the mount folder exists

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

add_email()[source]

Add a new e-mail adress

Arguments: None

Returns: None

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_settings()[source]

Get settings as dict

Arguments: None

Returns: Settings dictionary as list

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
update()[source]

Update the combo boxes.

Arguments: None

Returns: None

update_email()[source]

Update E-Mail file.

Arguments: None

Returns: None

update_telegram()[source]

Update telegram settings file

Arguments: None

Returns: None

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

change_tooltip(text)[source]
clear_combo()[source]

Remove all users from the combo box.

Arguments: None

Returns: None

get_settings()[source]

Get text of the currently selected combo item.

Arguments: None

Returns: Settings dictionary

set_settings(name, state)[source]

Set currently selected combo item in text.

Arguments: name - Name of the person that should be currently selected. state - State of the person (True/False;Enables/Disables)

Returns: None

update_combo(typ, users)[source]

Update the combo boxes.

Arguments: users - User dictionary

Returns: None

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/>.

class transphire.passworddialog.PasswordDialog(folder, default, login, extension, fixed_folder, parent=None)[source]

Bases: PyQt5.QtWidgets.QDialog

User password dialog

Inherits: QDialog

Signals: None

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

eventFilter(source, event)[source]

Override the QMainWindow eventFilter function.

source - Source that led to the event trigger event - Emitted event

Returns: True, if it has been a close event -> Redock widget Event, if it is another event

reset_plot()[source]
select_tab(widget)[source]
set_floating()[source]
set_visibility(visible, name)[source]
synchronize_tabs(widget)[source]
update_figure(name, name_no_feedback, data, directory_name, settings)[source]

Update the figure in the canvas

name - Name of the program that called this function. data - Data to plot. directory_name - Directory to save plots to. settings - TranSPHIRE settings

Returns: None

class transphire.plotcontainer.TwinContainer(dock_widget, *args, parent=None, **kwargs)[source]

Bases: PyQt5.QtWidgets.QWidget

add_to_layout(name, widget)[source]
handle_show(name, widget, state)[source]
mouse_twin_event(event)[source]

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

update_labels(title, label_x, label_y)[source]
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

add_canvas()[source]
clear_canvas()[source]
do_data_reset()[source]
force_update(do_message=False)[source]
hide_marker()[source]
hide_twin(state)[source]
static high_res(x_data, y_data, splits)[source]
prepare_axes(update)[source]
set_current_image_name(text)[source]
set_settings(name, name_no_feedback, data, directory_name, settings)[source]
setup_values()[source]
start_plotting()[source]
update_data(do_message=False)[source]
update_figure(do_message=False)[source]
update_helpers(canvas, plot_idx, update, plot_type)[source]
update_histogram(canvas, plot_idx, update)[source]
update_image()[source]
update_image_plot(canvas, data_x, data_y, high_res, label, marker, color, idx)[source]
update_trim()[source]
update_values(canvas, plot_idx, update)[source]
class transphire.plotwidget.SelectWidget(parent=None)[source]

Bases: PyQt5.QtWidgets.QWidget

check_enable(idx)[source]
filter_combo(text)[source]
get_value()[source]
handle_change()[source]
reset_values()[source]
set_values(value_list)[source]
sig_update
class transphire.plotwidget.TrimWidget(plot_typ, min_default_x, max_default_x, min_default_y, max_default_y, bin_default, parent=None)[source]

Bases: PyQt5.QtWidgets.QWidget

get_values()[source]
reset_values()[source]
set_state(state)[source]
set_values(value_dict)[source]
sig_hide
sig_set_state
sig_update
class transphire.plotwidget.ViewWidget(parent=None)[source]

Bases: PyQt5.QtWidgets.QWidget

sig_hide
update_label(label_dict)[source]

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)

calculate_array()[source]

Calculate array.

Returns: None

static calculate_array_now(name, name_no_feedback, directory_name, settings)[source]
reset_list()[source]
send_data(data)[source]
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/>.

class transphire.separator.Separator(typ, color, up=False, down=False, left=False, right=False, parent=None)[source]

Bases: PyQt5.QtWidgets.QWidget

Separator widget

hide_show_widget(status)[source]

Hide or show the widget with the status.

Arguments: status - Status show or status hide.

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

emit_global(_=None)[source]
emit_signals()[source]
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_input_names()[source]
get_settings(quiet=False)[source]

Get the settings as dict

Arguments: quiet - If True, no prints are executed

Returns: Settings as dictionary

prepare_send_adjust(text)[source]
search_for_projects(project_dir)[source]
set_design(settings)[source]

Set settings to the widgets

Arguments: settings - Settings to set.

Returns: None

set_global(global_dict)[source]
set_new_model(weights, threshold)[source]
set_settings(settings)[source]

Set settings to the widgets

Arguments: settings - Settings to set.

Returns: None

sig_adjust_tab
sig_change_use_movie
update_global(text)[source]

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

change_tooltip(text)[source]
enlarge()[source]
get_combo_entries()[source]

Get the entries of the combo boxes.

Arguments: None

Returns: List containing entries.

get_current_global()[source]
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.MyTabBar(parent)[source]

Bases: PyQt5.QtWidgets.QTabBar

paintEvent(self, QPaintEvent)[source]
tabSizeHint(self, int) → QSize[source]
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

assign_latest(idx)[source]
count()[source]

Return the number of tabs.

Arguments: None

Returns: Number of tabs

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]
order_tabs()[source]
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
tabText(idx)[source]

Return the text of the tab at idx

Arguments: idx - Index of the tab

Returns: Text of the tab at position isx

widget(idx)[source]

Return the widget that belongs to the idx of tabs.

Arguments: idx - Tab index

Returns: Widget

transphire.templatedialog module

class transphire.templatedialog.TemplateDialog(settings_directory, add_remove=True, parent=None)[source]

Bases: PyQt5.QtWidgets.QDialog

TemplateDialog dialog. Dialog used to enter the template.

Inherits from: QDialog

add_template()[source]
choose_template()[source]
copy_template()[source]
remove_template()[source]

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_global()[source]
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_content.default_unblur_v1_0_0()[source]

Content of Unblur version 1.0.0.

Arguments: None

Return: Content items as list

transphire.transphire_content.default_window_1_2()[source]

Content of sp_window version 1.2

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

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_import.import_window_v1_2(name, name_no_feedback, settings, directory_name, import_name='', send_data=None)[source]

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_box(jpg_data, maskcenters, box_size)[source]
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.create_filter_command(file_input, settings)[source]
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.dummy(data, settings, label)[source]
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_plot.update_micrograph(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_motion(data, settings, label)[source]

Update the plot for MotionCor2 v1.0.0.

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_train2d.create_restack_command(stack_name, output_dir, settings)[source]
transphire.transphire_train2d.create_substack_command(class_average_name, input_stack, isac_dir, output_dir, settings)[source]
transphire.transphire_train2d.create_train_command(sum_folder, box_folder, output_dir, name, settings)[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/>.

class transphire.transphire_utils.DataFrame(manager, file_path)[source]

Bases: object

append_values(*args, **kwargs)[source]
get_df(*args, **kwargs)[source]
get_index_where(*args, **kwargs)[source]
get_values(*args, **kwargs)[source]
load_df(*args, **kwargs)[source]
save_df(*args, **kwargs)[source]
set_df(*args, **kwargs)[source]
set_values(*args, **kwargs)[source]
value_in_column(*args, **kwargs)[source]
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.copytree(root_src_dir, root_dst_dir)[source]
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.get_unique_types()[source]
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.normalize_image(data, apix=1.0, min_res=30, real=True)[source]
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.rebin(arr, new_shape)[source]
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

transphire.transphire_utils.rerun_function_in_case_of_error(func)[source]
transphire.transphire_utils.split_maximum(text, max_char, split_char=None)[source]

Split text into chunks of size max_char containing whole words.

Arguments: text - Text to split max_char - Maximum number of characters

Returns: Splitted text

transphire.transphire_utils.thread_safe(func)[source]
transphire.transphire_utils.tooltip_style()[source]

Module contents