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ptycho_gui.py
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ptycho_gui.py
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import sys
import os
import random
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtWidgets import QFileDialog, QAction
from nsls2ptycho.ui import ui_ptycho
from nsls2ptycho.core.utils import clean_shared_memory, get_mpi_num_processes, parse_range
from nsls2ptycho.core.ptycho_param import Param
from nsls2ptycho.core.ptycho_recon import PtychoReconWorker, PtychoReconFakeWorker, HardWorker
from nsls2ptycho.core.ptycho_qt_utils import PtychoStream
from nsls2ptycho.core.widgets.mplcanvas import load_image_pil
from nsls2ptycho.core.ptycho.utils import parse_config
from nsls2ptycho._version import __version__
# databroker related
try:
from nsls2ptycho.core.HXN_databroker import hxn_db, load_metadata
from hxntools.scan_info import ScanInfo
except ImportError as ex:
print('[!] Unable to import hxntools-related packages some features will '
'be unavailable')
print('[!] (import error: {})'.format(ex))
from nsls2ptycho.reconStep_gui import ReconStepWindow
from nsls2ptycho.roi_gui import RoiWindow
from nsls2ptycho.scan_pt import ScanWindow
import h5py
import numpy as np
from numpy import pi
import traceback
# for frontend-backend communication
from posix_ipc import SharedMemory, ExistentialError
import mmap
# set True for testing GUI changes
_TEST = False
# for shared memory
mm_list = []
shm_list = []
class MainWindow(QtWidgets.QMainWindow, ui_ptycho.Ui_MainWindow):
_mainwindow_signal = QtCore.pyqtSignal()
def __init__(self, parent=None, param:Param=None):
super().__init__(parent)
self.setupUi(self)
QtWidgets.QApplication.setStyle('Plastique')
# connect
self.btn_load_probe.clicked.connect(self.loadProbe)
self.btn_load_object.clicked.connect(self.loadObject)
self.ck_init_prb_flag.clicked.connect(self.resetProbeFlg)
self.ck_init_obj_flag.clicked.connect(self.resetObjectFlg)
self.btn_choose_cwd.clicked.connect(self.setWorkingDirectory)
self.cb_dataloader.currentTextChanged.connect(self.setLoadButton)
self.btn_load_scan.clicked.connect(self.loadExpParam)
self.btn_view_frame.clicked.connect(self.viewDataFrame)
#self.le_scan_num.editingFinished.connect(self.forceLoad) # too sensitive, why?
self.le_scan_num.textChanged.connect(self.forceLoad)
self.cb_dataloader.currentTextChanged.connect(self.forceLoad)
self.cb_detectorkind.currentTextChanged.connect(self.forceLoad)
self.ck_mode_flag.clicked.connect(self.modeMultiSliceGuard)
self.ck_multislice_flag.clicked.connect(self.modeMultiSliceGuard)
self.ck_mask_obj_flag.clicked.connect(self.updateObjMaskFlg)
self.ck_gpu_flag.clicked.connect(self.updateGpuFlg)
self.ck_bragg_flag.clicked.connect(self.updateBraggFlg)
self.ck_pc_flag.clicked.connect(self.updatePcFlg)
self.ck_position_correction_flag.clicked.connect(self.updateCorrFlg)
self.ck_refine_data_flag.clicked.connect(self.updateRefineDataFlg)
self.ck_postprocessing_flag.clicked.connect(self.showNoPostProcessingWarning)
self.ck_batch_crop_flag.clicked.connect(self.updateBatchCropDataFlg)
self.cb_dataloader.currentTextChanged.connect(self.updateBatchCropDataFlg)
self.btn_recon_start.clicked.connect(self.start)
self.btn_recon_stop.clicked.connect(self.stop)
self.btn_recon_batch_start.clicked.connect(self.batchStart)
self.btn_recon_batch_stop.clicked.connect(self.batchStop)
self.ck_init_prb_batch_flag.stateChanged.connect(self.switchProbeBatch)
self.ck_init_obj_batch_flag.stateChanged.connect(self.switchObjectBatch)
self.menu_import_config.triggered.connect(self.importConfig)
self.menu_export_config.triggered.connect(self.exportConfig)
self.menu_clear_config_history.triggered.connect(self.removeConfigHistory)
self.menu_save_config_history.triggered.connect(self.saveConfigHistory)
self.actionClear_shared_memory.triggered.connect(self.clearSharedMemory)
self.btn_MPI_file.clicked.connect(self.setMPIfile)
self.le_gpus.textChanged.connect(self.resetMPIFlg)
# setup
self.sp_pha_max.setMaximum(pi)
self.sp_pha_max.setMinimum(-pi)
self.sp_pha_min.setMaximum(pi)
self.sp_pha_min.setMinimum(-pi)
# init.
if param is None:
self.param = Param() # default
else:
self.param = param
self._prb = None
self._obj = None
self._ptycho_gpu_thread = None
self._worker_thread = None
self._db = None # hold the Broker instance that contains the info of the given scan id
self._mds_table = None # hold a Pandas.dataframe instance
self._loaded = False # whether the user has loaded metadata or not (from either databroker or h5)
self._scan_numbers = None # a list of scan numbers for batch mode
self._scan_points = None # an array of shape (2, N) holding the scan coordinates
self._batch_prb_filename = None # probe's filename template for batch mode
self._batch_obj_filename = None # object's filename template for batch mode
self._config_path = os.path.expanduser("~") + "/.ptycho_gui/.ptycho_gui_config"
if not os.path.isdir(os.path.dirname(self._config_path)):
os.makedirs(os.path.dirname(self._config_path))
self.reconStepWindow = None
self.roiWindow = None
self.scanWindow = None
# temporary solutions
self.ck_ms_pie_flag.setEnabled(False)
self.ck_weak_obj_flag.setEnabled(False)
#self.cb_alg_flag. addItem("PIE")
#self.cb_alg2_flag.addItem("PIE")
# TODO: find a way to register the live windows so that they can be opened anytime
self.menuWindows.setEnabled(False)
#self.actionROI.setEnabled(False)
#self.actionMonitor.setEnabled(False)
#self.actionScan_points.setEnabled(False)
#if self.menu_save_config_history.isChecked(): # TODO: think of a better way...
self.retrieveConfigHistory()
self.update_gui_from_param()
self.updateModeFlg()
self.updateMultiSliceFlg()
self.updateObjMaskFlg()
self.updateBraggFlg()
self.updatePcFlg()
self.updateCorrFlg()
self.updateRefineDataFlg()
self.updateBatchCropDataFlg()
self.checkGpuAvail()
self.updateGpuFlg()
self.resetExperimentalParameters() # probably not necessary
self.setLoadButton()
# generate a unique string for shared memory
if sys.platform.startswith('darwin'): # OS X has a much shorter name limit
self.param.shm_name = os.getlogin()+'_'+str(os.getpid())+'_'+str(random.randrange(256))
else:
self.param.shm_name = 'ptycho_'+os.getlogin()+'_'+str(os.getpid())+'_'+str(random.randrange(256))
# TODO: delete param.shm_name read in from previous config so that we can reset the buttons earlier
self.resetButtons()
# display GUI version
self.setWindowTitle("NSLS-II Ptychography v" + __version__)
@property
def db(self):
# access the Broker instance; the name is probably not intuitive enough...?
return self._db
@db.setter
def db(self, scan_id:int):
# TODO: this should be configured based on selected beamline profile!
self._db = hxn_db
def resetButtons(self):
self.btn_recon_start.setEnabled(True)
self.btn_recon_stop.setEnabled(False)
self.btn_recon_batch_start.setEnabled(True)
self.btn_recon_batch_stop.setEnabled(False)
self.recon_bar.setValue(0)
# close the mmap arrays
# removing these arrays, can be changed later if needed
if self._prb is not None:
del self._prb
self._prb = None
if self._obj is not None:
del self._obj
self._obj = None
#if self._scan_points is not None:
# del self._scan_points
# self._scan_points = None
self.close_mmap()
# TODO: consider merging this function with importConfig()?
def retrieveConfigHistory(self):
if os.path.isfile(self._config_path):
try:
param = parse_config(self._config_path, Param())
self.menu_save_config_history.setChecked(param.save_config_history)
if param.save_config_history:
self.param = param
except Exception as ex:
self.exception_handler(ex)
def saveConfigHistory(self):
self.param.save_config_history = self.menu_save_config_history.isChecked()
def removeConfigHistory(self):
if os.path.isfile(self._config_path):
self.param = Param() # default
os.remove(self._config_path)
self.update_gui_from_param()
def update_param_from_gui(self):
p = self.param
# data group
p.scan_num = str(self.le_scan_num.text())
p.detectorkind = str(self.cb_detectorkind.currentText())
p.frame_num = int(self.sp_fram_num.value())
# p.working_directory set by setWorkingDirectory()
# Exp param group
p.xray_energy_kev = float(self.sp_xray_energy.value())
if self.sp_xray_energy.value() != 0.:
p.lambda_nm = 1.2398/self.sp_xray_energy.value()
p.z_m = float(self.sp_detector_distance.value())
p.nx = int(self.sp_x_arr_size.value()) # bookkeeping
p.dr_x = float(self.sp_x_step_size.value())
p.x_range = float(self.sp_x_scan_range.value())
p.ny = int(self.sp_y_arr_size.value()) # bookkeeping
p.dr_y = float(self.sp_y_step_size.value())
p.y_range = float(self.sp_y_scan_range.value())
#p.scan_type = str(self.cb_scan_type.currentText()) # do we need this one?
p.nz = int(self.sp_num_points.value()) # bookkeeping
# recon param group
p.n_iterations = int(self.sp_n_iterations.value())
p.alg_flag = str(self.cb_alg_flag.currentText())
p.alg2_flag = str(self.cb_alg2_flag.currentText())
p.alg_percentage = float(self.sp_alg_percentage.value())
p.sign = str(self.le_sign.text())
p.precision = self.cb_precision_flag.currentText()
p.init_prb_flag = self.ck_init_prb_flag.isChecked()
p.init_obj_flag = self.ck_init_obj_flag.isChecked()
# prb and obj path already set
p.mode_flag = self.ck_mode_flag.isChecked()
p.prb_mode_num = self.sp_prb_mode_num.value()
p.obj_mode_num = self.sp_obj_mode_num.value()
if p.mode_flag and "_mode" not in p.sign:
p.sign = p.sign + "_mode"
p.multislice_flag = self.ck_multislice_flag.isChecked()
p.slice_num = int(self.sp_slice_num.value())
p.slice_spacing_m = float(self.sp_slice_spacing_m.value() * 1e-6)
if p.multislice_flag and "_ms" not in p.sign:
p.sign = p.sign + "_ms"
p.amp_min = float(self.sp_amp_min.value())
p.amp_max = float(self.sp_amp_max.value())
p.pha_min = float(self.sp_pha_min.value())
p.pha_max = float(self.sp_pha_max.value())
p.gpu_flag = self.ck_gpu_flag.isChecked()
p.gpus = parse_range(self.le_gpus.text(), reverse_sort=False)
p.gpu_batch_size = int(self.cb_gpu_batch_size.currentText())
# adv param group
p.ccd_pixel_um = float(self.sp_ccd_pixel_um.value())
p.distance = float(self.sp_distance.value())
p.angle_correction_flag = self.ck_angle_correction_flag.isChecked()
p.x_direction = float(self.sp_x_direction.value())
p.y_direction = float(self.sp_y_direction.value())
p.angle = self.sp_angle.value()
p.start_update_probe = self.sp_start_update_probe.value()
p.start_update_object = self.sp_start_update_object.value()
p.ml_mode = self.cb_ml_mode.currentText()
p.ml_weight = self.sp_ml_weight.value()
p.dm_version = self.sp_dm_version.value()
p.cal_scan_pattern_flag = self.ck_cal_scal_pattern_flag.isChecked()
p.nth = self.sp_nth.value()
p.start_ave = self.sp_start_ave.value()
p.processes = self.sp_processes.value()
p.bragg_flag = self.ck_bragg_flag.isChecked()
p.bragg_theta = self.sp_bragg_theta.value()
p.bragg_gamma = self.sp_bragg_gamma.value()
p.bragg_delta = self.sp_bragg_delta.value()
p.pc_flag = self.ck_pc_flag.isChecked()
p.pc_sigma = self.sp_pc_sigma.value()
p.pc_alg = self.cb_pc_alg.currentText()
p.pc_kernel_n = self.sp_pc_kernel_n.value()
p.position_correction_flag = self.ck_position_correction_flag.isChecked()
p.position_correction_start = self.sp_position_correction_start.value()
p.position_correction_step = self.sp_position_correction_step.value()
p.sigma2 = float(self.sp_sigma2.value())
p.beta = float(self.sp_beta.value())
p.display_interval = int(self.sp_display_interval.value())
p.preview_flag = self.ck_preview_flag.isChecked()
p.cal_error_flag = self.ck_cal_error_flag.isChecked()
p.prb_center_flag = self.ck_prb_center_flag.isChecked()
p.mask_obj_flag = self.ck_mask_obj_flag.isChecked()
p.norm_prb_amp_flag = self.ck_norm_prb_amp_flag.isChecked()
p.weak_obj_flag = self.ck_weak_obj_flag.isChecked()
p.ms_pie_flag = self.ck_ms_pie_flag.isChecked()
p.refine_data_flag = self.ck_refine_data_flag.isChecked()
p.refine_data_start_it = int(self.sp_refine_data_start_it.value())
p.refine_data_interval = int(self.sp_refine_data_interval.value())
p.refine_data_step = float(self.sp_refine_data_step.value())
p.profiler_flag = self.ck_profiler_flag.isChecked()
p.postprocessing_flag = self.ck_postprocessing_flag.isChecked()
p.use_NCCL = self.rb_nccl.isChecked()
p.use_CUDA_MPI = self.rb_cuda_mpi.isChecked()
# TODO: organize them
#self.ck_init_obj_dpc_flag.setChecked(p.init_obj_dpc_flag)
#self.ck_mask_prb_flag.setChecked(p.mask_prb_flag)
#self.ck_mesh_flag.setChecked(p.mesh_flag)
#self.ck_sf_flag.setChecked(p.sf_flag)
# batch param group, necessary?
def update_gui_from_param(self):
p = self.param
# Data group
self.le_scan_num.setText(p.scan_num)
self.le_working_directory.setText(str(p.working_directory or ''))
self.cb_detectorkind.setCurrentIndex(p.get_detector_kind_index())
self.sp_fram_num.setValue(int(p.frame_num))
# Exp param group
self.sp_xray_energy.setValue(1.2398/float(p.lambda_nm) if 'lambda_nm' in p.__dict__ else 0.)
self.sp_detector_distance.setValue(float(p.z_m) if 'z_m' in p.__dict__ else 0)
self.sp_x_arr_size.setValue(float(p.nx))
self.sp_x_step_size.setValue(float(p.dr_x))
self.sp_x_scan_range.setValue(float(p.x_range))
self.sp_y_arr_size.setValue(float(p.ny))
self.sp_y_step_size.setValue(float(p.dr_y))
self.sp_y_scan_range.setValue(float(p.y_range))
self.cb_scan_type.setCurrentIndex(p.get_scan_type_index())
self.sp_num_points.setValue(int(p.nz))
# recon param group
self.sp_n_iterations.setValue(int(p.n_iterations))
self.cb_alg_flag.setCurrentIndex(p.get_alg_flg_index())
self.cb_alg2_flag.setCurrentIndex(p.get_alg2_flg_index())
self.sp_alg_percentage.setValue(float(p.alg_percentage))
self.le_sign.setText(p.sign)
self.cb_precision_flag.setCurrentText(p.precision)
self.ck_init_prb_flag.setChecked(p.init_prb_flag)
self.le_prb_path.setText(str(p.prb_filename or ''))
self.ck_init_obj_flag.setChecked(p.init_obj_flag)
self.le_obj_path.setText(str(p.obj_filename or ''))
self.ck_mode_flag.setChecked(p.mode_flag)
self.sp_prb_mode_num.setValue(int(p.prb_mode_num))
self.sp_obj_mode_num.setValue(int(p.obj_mode_num))
self.ck_multislice_flag.setChecked(p.multislice_flag)
self.sp_slice_num.setValue(int(p.slice_num))
self.sp_slice_spacing_m.setValue(p.get_slice_spacing_m())
self.sp_amp_max.setValue(float(p.amp_max))
self.sp_amp_min.setValue(float(p.amp_min))
self.sp_pha_max.setValue(float(p.pha_max))
self.sp_pha_min.setValue(float(p.pha_min))
self.ck_gpu_flag.setChecked(p.gpu_flag)
gpu_str = ''
for i, dev_id in enumerate(p.gpus):
gpu_str += str(dev_id)
if i != len(p.gpus) - 1:
gpu_str += ', '
self.le_gpus.setText(gpu_str)
self.cb_gpu_batch_size.setCurrentIndex(p.get_gpu_batch_index())
# set MPI file path from param
if p.mpi_file_path != '':
mpi_filename = os.path.basename(p.mpi_file_path)
self.le_MPI_file_path.setText(mpi_filename)
# TODO: does this make sense?
self.le_gpus.setText('')
# adv param group
self.sp_ccd_pixel_um.setValue(p.ccd_pixel_um)
self.sp_distance.setValue(float(p.distance))
self.ck_angle_correction_flag.setChecked(p.angle_correction_flag)
self.sp_x_direction.setValue(p.x_direction)
self.sp_y_direction.setValue(p.y_direction)
self.sp_angle.setValue(p.angle)
self.sp_start_update_probe.setValue(p.start_update_probe)
self.sp_start_update_object.setValue(p.start_update_object)
self.cb_ml_mode.setCurrentText(p.ml_mode)
self.sp_ml_weight.setValue(p.ml_weight)
self.sp_dm_version.setValue(p.dm_version)
self.ck_cal_scal_pattern_flag.setChecked(p.cal_scan_pattern_flag)
self.sp_nth.setValue(p.nth)
self.sp_start_ave.setValue(p.start_ave)
self.sp_processes.setValue(p.processes)
self.ck_bragg_flag.setChecked(p.bragg_flag)
self.sp_bragg_theta.setValue(p.bragg_theta)
self.sp_bragg_gamma.setValue(p.bragg_gamma)
self.sp_bragg_delta.setValue(p.bragg_delta)
self.ck_pc_flag.setChecked(p.pc_flag)
self.sp_pc_sigma.setValue(p.pc_sigma)
self.cb_pc_alg.setCurrentText(p.pc_alg)
self.sp_pc_kernel_n.setValue(p.pc_kernel_n)
self.ck_position_correction_flag.setChecked(p.position_correction_flag)
self.sp_position_correction_start.setValue(p.position_correction_start)
self.sp_position_correction_step.setValue(p.position_correction_step)
self.sp_sigma2.setValue(p.sigma2)
self.sp_beta.setValue(p.beta)
self.sp_display_interval.setValue(p.display_interval)
self.ck_preview_flag.setChecked(p.preview_flag)
self.ck_cal_error_flag.setChecked(p.cal_error_flag)
self.ck_init_obj_dpc_flag.setChecked(p.init_obj_dpc_flag)
self.ck_prb_center_flag.setChecked(p.prb_center_flag)
self.ck_mask_prb_flag.setChecked(p.mask_prb_flag)
self.ck_mask_obj_flag.setChecked(p.mask_obj_flag)
self.ck_norm_prb_amp_flag.setChecked(p.norm_prb_amp_flag)
self.ck_weak_obj_flag.setChecked(p.weak_obj_flag)
self.ck_mesh_flag.setChecked(p.mesh_flag)
self.ck_ms_pie_flag.setChecked(p.ms_pie_flag)
self.ck_sf_flag.setChecked(p.sf_flag)
self.ck_refine_data_flag.setChecked(p.refine_data_flag)
self.sp_refine_data_start_it.setValue(p.refine_data_start_it)
self.sp_refine_data_interval.setValue(p.refine_data_interval)
self.sp_refine_data_step.setValue(p.refine_data_step)
self.ck_profiler_flag.setChecked(p.profiler_flag)
self.ck_postprocessing_flag.setChecked(p.postprocessing_flag)
self.rb_nccl.setChecked(p.use_NCCL)
self.rb_cuda_mpi.setChecked(p.use_CUDA_MPI)
# batch param group, necessary?
def start(self, batch_mode=False):
if self._ptycho_gpu_thread is not None and self._ptycho_gpu_thread.isFinished():
self._ptycho_gpu_thread = None
if self._ptycho_gpu_thread is None:
if not self._loaded:
print("[WARNING] Remember to click \"Load\" before proceeding!", file=sys.stderr)
return
self.update_param_from_gui() # this has to be done first, so all operations depending on param are correct
self.recon_bar.setValue(0)
self.recon_bar.setMaximum(self.param.n_iterations)
# at least one GPU needs to be selected
if self.param.gpu_flag and len(self.param.gpus) == 0 and self.param.mpi_file_path == '':
print("[WARNING] select at least one GPU!", file=sys.stderr)
return
# batch mode requires some additional changes to param
if batch_mode:
if self._batch_prb_filename is not None:
p = self.param
p.init_prb_flag = False
scan_num = str(self.param.scan_num)
sign = self._batch_prb_filename[1].split('probe')[0]
sign = sign.strip('_')
dirname = p.working_directory + "/recon_result/S" + scan_num + "/" + sign + "/recon_data/"
filename = scan_num.join(self._batch_prb_filename)
p.set_prb_path(dirname, filename)
print("[BATCH] will load " + dirname + filename + " as probe")
if self._batch_obj_filename is not None:
p = self.param
p.init_obj_flag = False
scan_num = str(self.param.scan_num)
sign = self._batch_obj_filename[1].split('object')[0]
sign = sign.strip('_')
dirname = p.working_directory + "/recon_result/S" + scan_num + "/" + sign + "/recon_data/"
filename = scan_num.join(self._batch_obj_filename)
p.set_obj_path(dirname, filename)
print("[BATCH] will load " + dirname + filename + " as object")
# this is needed because MPI processes need to know the working directory...
self._exportConfigHelper(self._config_path)
# init reconStepWindow
if self.ck_preview_flag.isChecked():
if self.param.mode_flag:
info = (self.param.obj_mode_num, self.param.prb_mode_num, 1)
elif self.param.multislice_flag:
info = (self.param.slice_num, 1, 1)
else:
info = (1, 1, 2)
if self.reconStepWindow is None:
self.reconStepWindow = ReconStepWindow(*info)
self.reconStepWindow.reset_window(*info, iterations=self.param.n_iterations,
slider_interval=self.param.display_interval)
self.reconStepWindow.show()
else:
if self.reconStepWindow is not None:
# TODO: maybe a thorough cleanup???
self.reconStepWindow.close()
if not _TEST:
thread = self._ptycho_gpu_thread = PtychoReconWorker(self.param, parent=self)
else:
thread = self._ptycho_gpu_thread = PtychoReconFakeWorker(self.param, parent=self)
thread.update_signal.connect(self.update_recon_step)
thread.finished.connect(self.resetButtons)
if batch_mode:
thread.finished.connect(self._batch_manager)
#thread.finished.connect(self.reconStepWindow.debug)
thread.start()
self.btn_recon_stop.setEnabled(True)
self.btn_recon_start.setEnabled(False)
# init scan window
# TODO: optimize and refactor this part
if self.ck_scan_pt_flag.isChecked():
if self.scanWindow is None:
self.scanWindow = ScanWindow()
self.scanWindow.reset_window()
self.scanWindow.show()
else:
if self.scanWindow is not None:
self.scanWindow.close()
self.scanWindow = None
return
if self._scan_points is None:
raise RuntimeError("Scan points were not read. This shouldn't happen. Abort.")
else:
self._scan_points[0] *= -1.*self.param.x_direction
self._scan_points[1] *= self.param.y_direction
# borrowed from nsls2ptycho/core/ptycho_recon.py
if self.param.mpi_file_path == '':
if self.param.gpu_flag:
num_processes = str(len(self.param.gpus))
else:
num_processes = str(self.param.processes) if self.param.processes > 1 else str(1)
else:
# regardless if GPU is used or not --- trust users to know this
num_processes = str(get_mpi_num_processes(self.param.mpi_file_path))
self.scanWindow.update_image(self._scan_points, int(num_processes))
def stop(self, batch_mode=False):
if self._ptycho_gpu_thread is not None:
if batch_mode:
self._ptycho_gpu_thread.finished.disconnect(self._batch_manager)
if self._ptycho_gpu_thread.isRunning():
self._ptycho_gpu_thread.kill() # first kill the mpi processes
self._ptycho_gpu_thread.quit() # then quit QThread gracefully
self._ptycho_gpu_thread = None
self.resetButtons()
if self.reconStepWindow is not None:
self.reconStepWindow.reset_window()
if self.scanWindow is not None:
self.scanWindow.reset_window()
def init_mmap(self):
p = self.param
datasize = 8 if p.precision == 'single' else 16
datatype = np.complex64 if p.precision == 'single' else np.complex128
global mm_list, shm_list
for i, name in enumerate(["/"+p.shm_name+"_obj_size", "/"+p.shm_name+"_prb", "/"+p.shm_name+"_obj"]):
shm_list.append(SharedMemory(name))
mm_list.append(mmap.mmap(shm_list[i].fd, shm_list[i].size))
nx_obj = int.from_bytes(mm_list[0].read(8), byteorder='big')
ny_obj = int.from_bytes(mm_list[0].read(8), byteorder='big') # the file position has been moved by 8 bytes when we get nx_obj
if p.mode_flag:
self._prb = np.ndarray(shape=(p.n_iterations, p.prb_mode_num, p.nx, p.ny), dtype=datatype, buffer=mm_list[1], order='C')
self._obj = np.ndarray(shape=(p.n_iterations, p.obj_mode_num, nx_obj, ny_obj), dtype=datatype, buffer=mm_list[2], order='C')
elif p.multislice_flag:
self._prb = np.ndarray(shape=(p.n_iterations, 1, p.nx, p.ny), dtype=datatype, buffer=mm_list[1], order='C')
self._obj = np.ndarray(shape=(p.n_iterations, p.slice_num, nx_obj, ny_obj), dtype=datatype, buffer=mm_list[2], order='C')
else:
self._prb = np.ndarray(shape=(p.n_iterations, 1, p.nx, p.ny), dtype=datatype, buffer=mm_list[1], order='C')
self._obj = np.ndarray(shape=(p.n_iterations, 1, nx_obj, ny_obj), dtype=datatype, buffer=mm_list[2], order='C')
def close_mmap(self):
# We close shared memory as long as the backend is terminated either normally or
# abnormally. The subtlety here is that the monitor should still be able to access
# the intermediate results after mmaps' are closed. A potential segfault is avoided
# by accessing the transformed results, which are buffered, not the original ones.
try:
global mm_list, shm_list
for mm, shm in zip(mm_list, shm_list):
mm.close()
shm.close_fd()
shm.unlink()
mm_list = []
shm_list = []
except NameError:
# either not using GUI, monitor is turned off, global variables are deleted or not yet created!
# need to examine the last case
try:
SharedMemory("/"+self.param.shm_name+"_obj_size").unlink()
SharedMemory("/"+self.param.shm_name+"_prb").unlink()
SharedMemory("/"+self.param.shm_name+"_obj").unlink()
except ExistentialError:
pass # nothing to clean up, we're done
def update_recon_step(self, it, data=None):
self.recon_bar.setValue(it)
if self.reconStepWindow is not None:
self.reconStepWindow.update_iter(it)
if not _TEST and self.ck_preview_flag.isChecked():
try:
if it == -1 and data == 'init_mmap':
try:
# the two npy are created by ptycho by this time
self.init_mmap()
except ExistentialError:
# user may kill the process prematurely
self.stop()
elif it == self.param.n_iterations+1:
# reserve it=n_iterations+1 as the working space
self.reconStepWindow.current_max_iters = self.param.n_iterations
p = self.param
if not p.postprocessing_flag:
return
work_dir = p.working_directory
scan_num = str(p.scan_num)
data_dir = work_dir+'/recon_result/S'+scan_num+'/'+p.sign+'/recon_data/'
data = {}
images = []
print("[SUCCESS] generated results are loaded in the preview window. ", end='', file=sys.stderr)
print("Slide to frame "+str(p.n_iterations+1)+" and select from drop-down menus.", file=sys.stderr)
if self.param.mode_flag:
# load data that has been averaged + orthonormalized + phase-ramp removed
for i in range(self.param.obj_mode_num):
data['obj_'+str(i)] = np.load(data_dir+'recon_'+scan_num+'_'+p.sign+'_' \
+'object_mode_orth_ave_rp_mode_'+str(i)+'.npy')
self.reconStepWindow.cb_image_object.addItem("Object "+str(i)+" (orth_ave_rp)")
# hard-wire the padding values here...
images.append( np.rot90(np.angle(data['obj_'+str(i)][(p.nx+30)//2:-(p.nx+30)//2, (p.ny+30)//2:-(p.ny+30)//2])) )
images.append( np.rot90(np.abs(data['obj_'+str(i)][(p.nx+30)//2:-(p.nx+30)//2, (p.ny+30)//2:-(p.ny+30)//2])) )
for i in range(self.param.prb_mode_num):
data['prb_'+str(i)] = np.load(data_dir+'recon_'+scan_num+'_'+p.sign+'_' \
+'probe_mode_orth_ave_rp_mode_'+str(i)+'.npy')
self.reconStepWindow.cb_image_probe.addItem("Probe "+str(i)+" (orth_ave_rp)")
images.append( np.rot90(np.abs(data['prb_'+str(i)])) )
images.append( np.rot90(np.angle(data['prb_'+str(i)])) )
elif self.param.multislice_flag:
# load data that has been averaged + phase-ramp removed
for i in range(self.param.slice_num):
data['obj_'+str(i)] = np.load(data_dir+'recon_'+scan_num+'_'+p.sign+'_' \
+'object_ave_rp_ms_'+str(i)+'.npy')
self.reconStepWindow.cb_image_object.addItem("Object "+str(i)+" (ave_rp)")
# hard-wire the padding values here...
images.append( np.rot90(np.angle(data['obj_'+str(i)][(p.nx+30)//2:-(p.nx+30)//2, (p.ny+30)//2:-(p.ny+30)//2])) )
images.append( np.rot90(np.abs(data['obj_'+str(i)][(p.nx+30)//2:-(p.nx+30)//2, (p.ny+30)//2:-(p.ny+30)//2])) )
for i in range(self.param.slice_num):
data['prb_'+str(i)] = np.load(data_dir+'recon_'+scan_num+'_'+p.sign+'_' \
+'probe_ave_rp_ms_'+str(i)+'.npy')
self.reconStepWindow.cb_image_probe.addItem("Probe "+str(i)+" (ave_rp)")
images.append( np.rot90(np.abs(data['prb_'+str(i)])) )
images.append( np.rot90(np.angle(data['prb_'+str(i)])) )
else:
# load data (ave & ave_rp)
for sol in ['ave', 'ave_rp']:
for tar, target in zip(['obj', 'prb'], ['object', 'probe']):
data[tar+'_'+sol] = np.load(data_dir+'recon_'+scan_num+'_'+p.sign+'_'+target+'_'+sol+'.npy')
# calculate images
for sol in ['ave', 'ave_rp']:
self.reconStepWindow.cb_image_object.addItem("Object ("+sol+")")
# hard-wire the padding values here...
images.append( np.rot90(np.angle(data['obj_'+sol][(p.nx+30)//2:-(p.nx+30)//2, (p.ny+30)//2:-(p.ny+30)//2])) )
images.append( np.rot90(np.abs(data['obj_'+sol][(p.nx+30)//2:-(p.nx+30)//2, (p.ny+30)//2:-(p.ny+30)//2])) )
for sol in ['ave', 'ave_rp']:
self.reconStepWindow.cb_image_probe.addItem("Probe ("+sol+")")
images.append( np.rot90(np.abs(data['prb_'+sol])) )
images.append( np.rot90(np.angle(data['prb_'+sol])) )
self.reconStepWindow.update_images(it, images)
elif (it-1) % self.param.display_interval == 0:
if self.param.mode_flag:
images = []
for i in range(self.param.obj_mode_num):
images.append(np.rot90(np.angle(self._obj[it-1, i])))
images.append(np.rot90(np.abs(self._obj[it-1, i])))
for i in range(self.param.prb_mode_num):
images.append(np.rot90(np.abs(self._prb[it-1, i])))
images.append(np.rot90(np.angle(self._prb[it-1, i])))
elif self.param.multislice_flag:
images = []
for i in range(self.param.slice_num):
images.append(np.rot90(np.angle(self._obj[it-1, i])))
images.append(np.rot90(np.abs(self._obj[it-1, i])))
#TODO: decide which probe we'd like to present
images.append(np.rot90(np.abs(self._prb[it-1, 0])))
images.append(np.rot90(np.angle(self._prb[it-1, 0])))
else:
images = [np.rot90(np.angle(self._obj[it-1, 0])),
np.rot90(np.abs(self._obj[it-1, 0] )),
np.rot90(np.abs(self._prb[it-1, 0] )),
np.rot90(np.angle(self._prb[it-1, 0]))]
self.reconStepWindow.update_images(it, images)
self.reconStepWindow.update_metric(it, data)
except TypeError as ex: # when MPI processes are terminated, _prb and _obj are deleted and so not subscriptable
pass
else:
# -------------------- Sungsoo version -------------------------------------
# a list of random images for test
# in the order of [object_amplitude, object_phase, probe_amplitude, probe_phase]
images = [np.random.random((128,128)) for _ in range(4)]
self.reconStepWindow.update_images(it, images)
self.reconStepWindow.update_metric(it, data)
def loadProbe(self):
filename, _ = QFileDialog.getOpenFileName(self, 'Open probe file', directory=self.param.working_directory, filter="(*.npy)")
if filename is not None and len(filename) > 0:
prb_filename = os.path.basename(filename)
prb_dir = filename[:(len(filename)-len(prb_filename))]
self.param.set_prb_path(prb_dir, prb_filename)
self.le_prb_path.setText(prb_filename)
self.ck_init_prb_flag.setChecked(False)
def resetProbeFlg(self):
# called when "estimate from data" is clicked
self.param.set_prb_path('', '')
self.le_prb_path.setText('')
self.ck_init_prb_flag.setChecked(True)
def loadObject(self):
filename, _ = QFileDialog.getOpenFileName(self, 'Open object file', directory=self.param.working_directory, filter="(*.npy)")
if filename is not None and len(filename) > 0:
obj_filename = os.path.basename(filename)
obj_dir = filename[:(len(filename)-len(obj_filename))]
self.param.set_obj_path(obj_dir, obj_filename)
self.le_obj_path.setText(obj_filename)
self.ck_init_obj_flag.setChecked(False)
def resetObjectFlg(self):
# called when "random start" is clicked
self.param.set_obj_path('', '')
self.le_obj_path.setText('')
self.ck_init_obj_flag.setChecked(True)
def setWorkingDirectory(self):
dirname = QFileDialog.getExistingDirectory(self, 'Choose working folder', directory=os.path.expanduser("~"))
if dirname is not None and len(dirname) > 0:
dirname = dirname + "/"
self.param.set_working_directory(dirname)
self.le_working_directory.setText(dirname)
def modeMultiSliceGuard(self):
'''
Currently our ptycho code does not support simultaneous mode + multi-slice reconstruction.
This function can be removed once the support is added.
'''
if self.ck_mode_flag.isChecked() and self.ck_multislice_flag.isChecked():
message = "Currently our ptycho code does not support simultaneous multi-mode + multi-slice reconstruction."
print("[WARNING] " + message, file=sys.stderr)
QtWidgets.QMessageBox.warning(self, "Warning", message)
self.ck_mode_flag.setChecked(False)
self.ck_multislice_flag.setChecked(False)
self.updateModeFlg()
self.updateMultiSliceFlg()
def updateModeFlg(self):
mode_flag = self.ck_mode_flag.isChecked()
self.sp_prb_mode_num.setEnabled(mode_flag)
self.sp_obj_mode_num.setEnabled(mode_flag)
self.param.mode_flag = mode_flag
def updateMultiSliceFlg(self):
flag = self.ck_multislice_flag.isChecked()
self.sp_slice_num.setEnabled(flag)
self.sp_slice_spacing_m.setEnabled(flag)
self.param.multislice_flag = flag
def updateObjMaskFlg(self):
mask_flag = self.ck_mask_obj_flag.isChecked()
self.sp_amp_min.setEnabled(mask_flag)
self.sp_amp_max.setEnabled(mask_flag)
self.sp_pha_min.setEnabled(mask_flag)
self.sp_pha_max.setEnabled(mask_flag)
self.param.mask_obj_flag = mask_flag
def checkGpuAvail(self):
try:
import cupy
except ImportError:
print('[!] Unable to import CuPy. GPU reconstruction is disabled.')
print('[!] (Either CuPy is not installed, or GPU is not available.)')
self.ck_gpu_flag.setChecked(False)
self.ck_gpu_flag.setEnabled(False)
self.param.gpu_flag = False
self.le_gpus.setText('')
self.le_gpus.setEnabled(False)
self.cb_gpu_batch_size.setEnabled(False)
def updateGpuFlg(self):
flag = self.ck_gpu_flag.isChecked()
self.le_gpus.setEnabled(flag)
self.rb_nccl.setEnabled(flag)
if not flag and self.rb_nccl.isChecked():
self.rb_mpi.setChecked(True)
def updateBraggFlg(self):
flag = self.ck_bragg_flag.isChecked()
self.sp_bragg_theta.setEnabled(flag)
self.sp_bragg_gamma.setEnabled(flag)
self.sp_bragg_delta.setEnabled(flag)
self.param.bragg_flag = flag
def updatePcFlg(self):
flag = self.ck_pc_flag.isChecked()
self.sp_pc_sigma.setEnabled(flag)
self.sp_pc_kernel_n.setEnabled(flag)
self.cb_pc_alg.setEnabled(flag)
self.param.pc_flag = flag
def updateCorrFlg(self):
flag = self.ck_position_correction_flag.isChecked()
self.sp_position_correction_start.setEnabled(flag)
self.sp_position_correction_step.setEnabled(flag)
self.param.position_correction_flag = flag
def updateRefineDataFlg(self):
flag = self.ck_refine_data_flag.isChecked()
self.sp_refine_data_start_it.setEnabled(flag)
self.sp_refine_data_interval.setEnabled(flag)
self.sp_refine_data_step.setEnabled(flag)
self.param.refine_data_flag = flag
def updateBatchCropDataFlg(self):
if self.cb_dataloader.currentText() != "Load from databroker":
flag = False
self.ck_batch_crop_flag.setChecked(flag)
self.ck_batch_crop_flag.setEnabled(flag)
else:
flag = self.ck_batch_crop_flag.isChecked()
self.ck_batch_crop_flag.setEnabled(True)
self.sp_batch_x0.setEnabled(flag)
self.sp_batch_y0.setEnabled(flag)
self.sp_batch_width.setEnabled(flag)
self.sp_batch_height.setEnabled(flag)
def showNoPostProcessingWarning(self):
if not self.ck_postprocessing_flag.isChecked():
print("[WARNING] Post-processing is turned off. No result will be written to disk!", file=sys.stderr)
def clearSharedMemory(self):
message = "Are you sure you want to clear the shared memory segments currently left in /dev/shm? "\
"The safest way to do so is to ensure you have only one window (that is, this one) opened on this machine."
ans = QtWidgets.QMessageBox.question(self, "Warning", message, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
if ans == QtWidgets.QMessageBox.Yes:
clean_shared_memory()
def setMPIfile(self):
filename, _ = QFileDialog.getOpenFileName(self, 'Open MPI machine file', directory=self.param.working_directory)
if filename is not None and len(filename) > 0:
mpi_filename = os.path.basename(filename)
mpi_dir = filename[:(len(filename)-len(mpi_filename))]
#self.param.le_MPI_file_path(mpi_dir, mpi_filename)
self.param.mpi_file_path = filename
#print(filename)
self.le_MPI_file_path.setText(mpi_filename)
self.le_gpus.setText('')
def resetMPIFlg(self):
# called when any gpu button is clicked
self.param.mpi_file_path = ''
self.le_MPI_file_path.setText('')
def batchStart(self):
if not self.ck_batch_crop_flag.isChecked() and not self.ck_batch_run_flag.isChecked():
print("[WARNING] Choose least one action (Crop or Run). Stop.", file=sys.stderr)
return
if self.cb_dataloader.currentText() == "Load from databroker":
if not self.ck_batch_crop_flag.isChecked():
print("[WARNING] Batch mode with databroker is set, but \"Crop data\" is not.\n"
"[WARNING] Will attempt to load h5 from working directory", file=sys.stderr)
try:
self._scan_numbers = parse_range(self.le_batch_items.text(), self.sp_batch_step.value())
print(self._scan_numbers)
# TODO: is there a way to lock all widgets to prevent accidental parameter changes in the middle?
# fire up
self.le_scan_num.textChanged.disconnect(self.forceLoad)
if self.ck_init_prb_batch_flag.isChecked():
filename = self.le_prb_path_batch.text()
self._batch_prb_filename = filename.split("*")
if self.ck_init_obj_batch_flag.isChecked():
filename = self.le_obj_path_batch.text()
self._batch_obj_filename = filename.split("*")
self._batch_manager() # serve as linked list's head
except Exception as ex:
self.exception_handler(ex)
def batchStop(self):
'''
Brute-force abortion of the entire batch. No resumption is possible.
'''
self._scan_numbers = None
self.le_scan_num.textChanged.connect(self.forceLoad)
self.stop(True)
if self.roiWindow is not None:
if self.roiWindow._worker_thread is not None:
self.roiWindow._worker_thread.disconnect()
## thread.terminate() freezes the whole GUI -- why?
#if self.roiWindow._worker_thread.isRunning():
# self.roiWindow._worker_thread.terminate()
# self.roiWindow._worker_thread.wait()
self.roiWindow._worker_thread = None
self.roiWindow = None
self.resetButtons()
def _batch_manager(self):
'''
This is a "linked list" that utilizes Qt's signal mechanism to retrieve the next item in the list
when the current item is processed. We need this because most likely the users want to put all
available computing resources to process the batch item by item, and having more than one worker
is not helping.
'''
# TODO: think what if anything goes wrong in the middle. Is this robust?
if self._scan_numbers is None:
return
if len(self._scan_numbers) > 0:
scan_num = self._scan_numbers.pop()
print("[BATCH] begin processing scan " + str(scan_num) + "...")
self.le_scan_num.setText(str(scan_num))
self.btn_recon_batch_start.setEnabled(False)
self.btn_recon_batch_stop.setEnabled(True)
if self.ck_batch_crop_flag.isChecked():
self._batch_crop() # also handles "Run" if needed