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Merge pull request #867 from bnmajor/update-llnl-import-workflow
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Update LLNL import workflow
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@joelvbernier
joelvbernier authored Apr 6, 2021
2 parents 0eae558 + d36a092 commit b8831b3
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Showing 5 changed files with 698 additions and 551 deletions.
5 changes: 3 additions & 2 deletions hexrd/ui/hexrd_config.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -422,7 +422,7 @@ def clear_images(self, initial_load=False):
self.load_panel_state.clear()
self.load_panel_state_reset.emit()

def load_instrument_config(self, path):
def load_instrument_config(self, path, import_raw=False):
old_detectors = self.detector_names

rme = self.rotation_matrix_euler()
Expand Down Expand Up @@ -470,7 +470,8 @@ def read_hexrd():
self.update_active_material_energy()
self.config['materials']['show_overlays'] = prev

self.instrument_config_loaded.emit()
if not import_raw:
self.instrument_config_loaded.emit()

new_detectors = self.detector_names
if old_detectors != new_detectors:
Expand Down
208 changes: 94 additions & 114 deletions hexrd/ui/import_data_panel.py
View file
Original file line number Diff line number Diff line change
@@ -1,21 +1,22 @@
import os
import yaml
import tempfile

from PySide2.QtCore import QObject, Signal
from PySide2.QtWidgets import QColorDialog, QFileDialog, QMessageBox
from PySide2.QtGui import QColor

from hexrd import resources as hexrd_resources

from hexrd.ui.utils import convert_tilt_convention
from hexrd.ui.hexrd_config import HexrdConfig
from hexrd.ui.image_file_manager import ImageFileManager
from hexrd.ui.image_load_manager import ImageLoadManager
from hexrd.ui.interactive_template import InteractiveTemplate
from hexrd.ui.load_images_dialog import LoadImagesDialog
from hexrd.ui import resource_loader
from hexrd.ui.ui_loader import UiLoader
from hexrd.ui.constants import UI_TRANS_INDEX_ROTATE_90
from hexrd.ui.constants import (
UI_TRANS_INDEX_ROTATE_90, UI_TRANS_INDEX_FLIP_HORIZONTALLY)

import hexrd.ui.resources.calibration

Expand All @@ -25,6 +26,8 @@ class ImportDataPanel(QObject):
# Emitted when new config is loaded
new_config_loaded = Signal()

cancel_workflow = Signal()

def __init__(self, cmap=None, parent=None):
super(ImportDataPanel, self).__init__(parent)

Expand All @@ -36,29 +39,32 @@ def __init__(self, cmap=None, parent=None):
self.canvas = parent.image_tab_widget.image_canvases[0]
self.detector_defaults = {}
self.cmap = cmap
self.detectors = []
self.editing = False

self.set_default_color()
self.setup_connections()

def setup_connections(self):
self.ui.instruments.currentIndexChanged.connect(
self.instrument_selected)
self.ui.detectors.currentIndexChanged.connect(self.detector_selected)
self.ui.load.clicked.connect(self.load_images)
self.ui.detectors.currentIndexChanged.connect(self.detector_selected)
self.ui.add_template.clicked.connect(self.add_template)
self.ui.trans.clicked.connect(self.setup_translate)
self.ui.rotate.clicked.connect(self.setup_rotate)
self.ui.add_transform.clicked.connect(self.add_transform)
self.ui.button_box.accepted.connect(self.crop_and_mask)
self.ui.button_box.rejected.connect(self.clear)
self.ui.save.clicked.connect(self.save_file)
self.ui.complete.clicked.connect(self.completed)
self.ui.bb_height.valueChanged.connect(self.update_bbox_height)
self.ui.bb_width.valueChanged.connect(self.update_bbox_width)
self.ui.line_style.currentIndexChanged.connect(
self.update_template_style)
self.ui.line_color.clicked.connect(self.pick_line_color)
self.ui.line_size.valueChanged.connect(self.update_template_style)
self.ui.cancel.clicked.connect(self.reset_panel)
self.ui.cancel.clicked.connect(self.cancel_workflow.emit)

def enable_widgets(self, *widgets, enabled):
for w in widgets:
Expand All @@ -79,27 +85,31 @@ def get_instrument_defaults(self):
fname = f'{self.instrument.lower()}_reference_config.yml'
text = resource_loader.load_resource(hexrd_resources, fname)
defaults = yaml.load(text, Loader=yaml.FullLoader)
self.detector_defaults['default_config'] = defaults
for det, vals in defaults['detectors'].items():
self.detector_defaults[det] = vals['transform']
self.detectors.append(det)

def instrument_selected(self, idx):
self.detectors.clear()
self.detector_defaults.clear()
instruments = {1: 'TARDIS', 2: 'PXRDIP'}
self.instrument = instruments.get(idx, None)

if self.instrument is None:
self.ui.detectors.setCurrentIndex(0)
self.ui.detectors.setDisabled(True)
self.enable_widgets(self.ui.file_selection, self.ui.transform_img,
enabled=False)
else:
self.get_instrument_defaults()
self.set_convention()
det_list = list(self.detector_defaults.keys())
det_list.insert(0, '(None)')
det_list = list(self.detectors)
self.load_instrument_config()
self.ui.detectors.clear()
self.ui.detectors.insertItems(0, det_list)
self.enable_widgets(self.ui.detector_label, self.ui.detectors,
enabled=True)
self.ui.detectors.addItems(det_list)
self.enable_widgets(self.ui.file_selection, enabled=True)
if self.instrument == 'PXRDIP':
HexrdConfig().load_panel_state['trans'] = (
[UI_TRANS_INDEX_FLIP_HORIZONTALLY])

def set_convention(self):
new_conv = {'axes_order': 'zxz', 'extrinsic': False}
Expand All @@ -111,34 +121,11 @@ def load_instrument_config(self):
hexrd.ui.resources.calibration, fname) as f:
for overlay in HexrdConfig().overlays:
overlay['visible'] = False
HexrdConfig().load_instrument_config(f)

def set_detector_defaults(self, det):
if det not in self.detector_defaults.keys():
return

for key, value in self.detector_defaults[det].items():
HexrdConfig().set_instrument_config_val(
['detectors', det, 'transform', key, 'value'], value)
eac = {'axes_order': 'zxz', 'extrinsic': False}
convert_tilt_convention(HexrdConfig().config['instrument'], None, eac)
self.detector_defaults[det]['tilt'] = (
HexrdConfig().get_instrument_config_val(
['detectors', det, 'transform', 'tilt', 'value']))
self.new_config_loaded.emit()
HexrdConfig().load_instrument_config(f, import_raw=True)

def detector_selected(self, selected):
self.ui.data.setEnabled(selected)
self.ui.instruments.setDisabled(selected)
if selected:
self.detector = self.ui.detectors.currentText()
old_det = HexrdConfig().detector_names[0]

self.cmap.block_updates(True)
HexrdConfig().rename_detector(old_det, self.detector)
self.cmap.block_updates(False)

self.set_detector_defaults(self.detector)
self.ui.instrument.setDisabled(selected)
self.detector = self.ui.detectors.currentText()

def update_bbox_height(self, val):
y0, y1, *x = self.it.bounds
Expand Down Expand Up @@ -183,31 +170,36 @@ def load_images(self):

file_names = [os.path.split(f[0])[1] for f in files]
self.ui.files_label.setText(', '.join(file_names))
self.enable_widgets(self.ui.outline, self.ui.add_template,
self.ui.transforms, self.ui.add_transform,
enabled=True)
self.enable_widgets(self.ui.transform_img, self.ui.association,
self.ui.finalize, enabled=True)
self.enable_widgets(self.parent().action_show_toolbar,
self.ui.save, enabled=False)
self.ui.instrument, enabled=False)
self.parent().action_show_toolbar.setChecked(False)

def add_transform(self):
# Prevent color map reset on transform
self.cmap.block_updates(True)
if self.it:
self.editing = True
self.clear_boundry()
ilm = ImageLoadManager()
ilm.set_state({'trans': [self.ui.transforms.currentIndex()]})
ilm.begin_processing(postprocess=True)
self.cmap.block_updates(False)

self.ui.transforms.setCurrentIndex(0)

img = HexrdConfig().image(self.detector, 0)
img = HexrdConfig().image('default', 0)
if self.detector in self.edited_images.keys():
# This transform is being done post-processing
self.edited_images[self.detector]['img'] = img
self.edited_images[self.detector]['height'] = img.shape[0]
self.edited_images[self.detector]['width'] = img.shape[1]

if self.it:
if self.editing:
self.add_template()

if self.it is not None:
self.it.update_image(img)

def display_bounds(self):
Expand All @@ -226,7 +218,7 @@ def display_bounds(self):

def add_template(self):
self.it = InteractiveTemplate(
HexrdConfig().image(self.detector, 0), self.parent())
HexrdConfig().image('default', 0), self.parent())
self.it.create_shape(
module=hexrd_resources,
file_name=f'{self.instrument}_{self.detector}_bnd.txt',
Expand All @@ -235,18 +227,12 @@ def add_template(self):
self.update_template_style()

self.display_bounds()
self.enable_widgets(self.ui.trans, self.ui.rotate, self.ui.button_box,
self.ui.complete, self.ui.line_color,
self.ui.line_style, self.ui.line_size,
self.ui.color_label, self.ui.size_label,
self.ui.style_label, enabled=True)
self.enable_widgets(self.ui.detectors, self.ui.add_template,
self.ui.load, self.ui.transforms,
self.ui.add_transform, enabled=False)
self.enable_widgets(self.ui.outline_position,
self.ui.outline_appearance, enabled=True)
self.enable_widgets(self.ui.association, self.ui.file_selection,
enabled=False)
if self.ui.instruments.currentText() != 'TARDIS':
self.enable_widgets(self.ui.height_label, self.ui.bb_height,
self.ui.bb_width, self.ui.width_label,
self.ui.bb_label, enabled=True)
self.ui.bbox.setEnabled(True)
self.ui.trans.setChecked(True)

def update_template_style(self):
Expand Down Expand Up @@ -294,54 +280,40 @@ def crop_and_mask(self):
self.it.disconnect_rotate()
self.finalize()
self.completed_detectors.append(self.detector)
self.enable_widgets(self.ui.detectors, self.ui.load, self.ui.complete,
self.ui.completed_dets, self.ui.save,
self.ui.finalize, self.ui.transforms,
self.ui.add_transform, enabled=True)
self.enable_widgets(self.ui.trans, self.ui.rotate, self.ui.button_box,
self.ui.add_template, self.ui.bb_label,
self.ui.bb_height, self.ui.height_label,
self.ui.bb_width, self.ui.width_label,
self.ui.line_color, self.ui.line_style,
self.ui.line_size, self.ui.color_label,
self.ui.size_label, self.ui.style_label,
enabled=False)
self.ui.completed_dets.setText(', '.join(
set(self.completed_detectors)))
self.enable_widgets(self.ui.association, self.ui.file_selection,
self.ui.transform_img, self.ui.complete,
enabled=True)
self.enable_widgets(self.ui.outline_appearance,
self.ui.outline_position, enabled=False)
self.ui.completed_dets.setText(
', '.join(set(self.completed_detectors)))

def finalize(self):
self.it.cropped_image
img = self.it.masked_image
detectors = self.detector_defaults['default_config'].get(
'detectors', {})
det = detectors.setdefault(self.detector, {})
width = det.setdefault('pixels', {}).get('columns', 0)
height = det.setdefault('pixels', {}).get('rows', 0)

ilm = ImageLoadManager()
self.cmap.block_updates(True)
# Do not re-apply transform if selected in load file dialog
HexrdConfig().load_panel_state.clear()
ilm.read_data([[img]], parent=self.ui)
if self.instrument == 'PXRDIP':
ilm.set_state({'trans': [UI_TRANS_INDEX_ROTATE_90]})
ilm.begin_processing(postprocess=True)
img = HexrdConfig().image(self.detector, 0)
self.cmap.block_updates(False)
# Boundary is currently rotated 90 degrees
width, height = height, width
self.it.cropped_image(height, width)

img = self.it.masked_image

self.edited_images[self.detector] = {
'img': img,
'height': img.shape[0],
'width': img.shape[1],
'tilt': self.it.rotation
}
self.clear_boundry()

def clear(self):
self.clear_boundry()
self.enable_widgets(self.ui.detectors, self.ui.load,
self.ui.add_template, self.ui.transforms,
self.ui.add_transform, enabled=True)
self.enable_widgets(self.ui.trans, self.ui.rotate, self.ui.button_box,
self.ui.save, self.ui.complete, enabled=False)

def save_file(self):
self.parent().action_save_imageseries.trigger()
self.enable_widgets(self.ui.association, self.ui.transform_img,
self.ui.file_selection, enabled=True)
self.enable_widgets(self.ui.outline_position,
self.ui.outline_appearance, enabled=False)

def check_for_unsaved_changes(self):
if self.it is None and self.detector in self.completed_detectors:
Expand All @@ -355,40 +327,48 @@ def check_for_unsaved_changes(self):

def reset_panel(self):
self.clear_boundry()
self.ui.instruments.setCurrentIndex(3)
self.ui.instruments.setCurrentIndex(0)
self.ui.detectors.setCurrentIndex(0)
self.ui.files_label.setText('')
self.ui.completed_dets.setText('')
self.enable_widgets(self.ui.detectors, self.ui.data, self.ui.outline,
self.ui.finalize, enabled=False)
self.completed_detectors = []
self.edited_images.clear()
self.ui.instrument.setEnabled(True)
self.enable_widgets(self.ui.association, self.ui.file_selection,
self.ui.transform_img, self.ui.outline_appearance,
self.ui.outline_position, self.ui.finalize,
enabled=False)
self.completed_detectors.clear()
self.detectors.clear()

def completed(self):
self.cmap.block_updates(True)
self.check_for_unsaved_changes()

files = []
HexrdConfig().rename_detector(self.detector, 'default')
for key, val in self.edited_images.items():
HexrdConfig().add_detector(key, 'default')
HexrdConfig().set_instrument_config_val(
['detectors', key, 'pixels', 'columns', 'value'],
int(val['width']))
HexrdConfig().set_instrument_config_val(
['detectors', key, 'pixels', 'rows', 'value'],
int(val['height']))
*zx, z = self.detector_defaults[key]['tilt']
HexrdConfig().set_instrument_config_val(
['detectors', key, 'transform', 'tilt', 'value'],
[*zx, (z + float(val['tilt']))])
translation = self.detector_defaults[key]['translation']
HexrdConfig().set_instrument_config_val(
['detectors', key, 'transform', 'translation', 'value'],
translation)
files.append([val['img']])
HexrdConfig().remove_detector('default')
self.new_config_loaded.emit()
detectors = self.detector_defaults['default_config'].get(
'detectors', {})
not_set = [d for d in detectors if d not in self.completed_detectors]
for det in not_set:
del(detectors[det])

for det in self.completed_detectors:
transform = detectors[det].setdefault('transform', {})
*zx, z = transform['tilt']
transform['tilt'] = (
[*zx, (z + float(self.edited_images[det]['tilt']))])
files.append([self.edited_images[det]['img']])

temp = tempfile.NamedTemporaryFile(delete=False, suffix='.yml')
data = yaml.dump(
self.detector_defaults['default_config'], sort_keys=False)
temp.write(data.encode('utf-8'))
temp.close()
HexrdConfig().load_instrument_config(temp.name)
self.set_convention()

if self.instrument == 'PXRDIP':
HexrdConfig().load_panel_state['trans'] = (
[UI_TRANS_INDEX_ROTATE_90] * len(self.detectors))
ImageLoadManager().read_data(files, parent=self.ui)

self.reset_panel()
Expand Down
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