class ScriptWindow(QDialog):
def __init__(self, parent=None):
super(ScriptWindow, self).__init__(parent)
self.setGeometry(100, 100, 800, 600)
self.parent = parent
font = QFontDatabase.systemFont(QFontDatabase.FixedFont)
font.setFixedPitch(True)
font.setPointSize(10)
self.editor = QPlainTextEdit()
self.editor.setFont(font)
self.editor.setTabStopWidth(self.editor.fontMetrics().width(" ") * 4)
self.highlight = PythonHighlighter(self.editor.document())
self.editor.setPlainText("# self.parent is the main GUI handle")
self.runScriptButton = QPushButton("Run script")
self.layout = QVBoxLayout()
self.layout.addWidget(self.editor)
self.layout.addWidget(self.runScriptButton)
self.setLayout(self.layout)
self.setWindowTitle("Script editor")
self.setup_button_behavior()
self.show()
def setup_button_behavior(self):
self.runScriptButton.clicked.connect(self.runscript)
def runscript(self):
print("Script is executed.")
print("Testing parent data accessibility")
text2execute = self.editor.toPlainText()
exec(text2execute)
class DefaultWidget(QWidget):
"""
The default widget for a repeating element.
It's a simple line edit with a label and an option required astrix.
"""
def __init__(
self,
label="",
line_name="na",
required=False,
placeholder_text=None,
spellings=True,
parent=None,
):
"""
Parameters
----------
label : str
The label that appears next to the text edit
line_name : str
The name to use for the text edit
required : boolean
Whethere to display the little blue required asterix
parent : QWidget
"""
QWidget.__init__(self, parent=parent)
self.layout = QHBoxLayout()
self.qlbl = QLabel(label, self)
self.added_line = QPlainTextEdit()
max_line_height = self.added_line.fontMetrics().height() + 10
self.added_line.setMaximumHeight(max_line_height)
self.added_line.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.added_line.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.added_line.mouseMoveEvent = self.mouse_move
self.added_line.setLineWrapMode(QPlainTextEdit.NoWrap)
self.added_line.textChanged.connect(self.remove_returns)
if spellings:
self.highlighter = Highlighter(self.added_line.document())
if not placeholder_text is None:
self.added_line.setPlaceholderText(placeholder_text)
self.added_line.setObjectName(line_name)
self.layout.addWidget(self.qlbl)
self.layout.addWidget(self.added_line)
if required:
self.required_label = QLabel(self)
font = QFont()
font.setFamily("Arial")
font.setPointSize(9)
font.setBold(False)
font.setItalic(False)
font.setWeight(50)
self.required_label.setFont(font)
self.required_label.setScaledContents(True)
self.required_label.setAlignment(QtCore.Qt.AlignHCenter
| QtCore.Qt.AlignVCenter)
self.required_label.setIndent(0)
self.required_label.setText(
QtCore.QCoreApplication.translate(
"",
'<html><head/><body><p align="center">'
'<span style=" font-size:18pt; color:#55aaff;">*'
"</span></p></body></html>",
))
self.layout.addWidget(self.required_label)
self.layout.setContentsMargins(1, 1, 1, 1)
self.layout.setSpacing(10)
self.setLayout(self.layout)
def mouse_move(self, e):
"""
over ride the mouse move event to ignore mouse movement (scrolling),
but only in the vertical dimension. Makes this plain text edit look and
feel like a line edit.
Parameters
----------
e : pyqt event
Returns
-------
None
"""
if e.y() < self.added_line.height() - 3 and e.x(
) < self.added_line.width() - 3:
QPlainTextEdit.mouseMoveEvent(self.added_line, e)
self.added_line.verticalScrollBar().setValue(
self.added_line.verticalScrollBar().minimum())
def remove_returns(self):
"""
After changes to the line, we need to make sure that the user has not entered any line returns, since the
single line is not intended to be a multiline string. Any line returns "\n" will be replace with a ' '
Returns
-------
None
"""
self.added_line.textChanged.disconnect()
old_position = self.added_line.textCursor().position()
curtext = self.added_line.toPlainText()
newtext = curtext.replace("\n", " ")
self.added_line.setPlainText(newtext)
cursor = self.added_line.textCursor()
cursor.setPosition(old_position)
self.added_line.setTextCursor(cursor)
self.added_line.textChanged.connect(self.remove_returns)
def setText(self, text):
utils.set_text(self.added_line, text)
cursor = self.added_line.textCursor()
cursor.setPosition(0)
self.added_line.setTextCursor(cursor)
def text(self):
return self.added_line.toPlainText()
class DefaultWidget(QWidget):
"""
The default widget for a repeating element.
It's a simple line edit with a label and an option required astrix.
"""
def __init__(self,
label='',
line_name='na',
required=False,
placeholder_text=None,
spellings=True,
parent=None):
"""
Parameters
----------
label : str
The label that appears next to the text edit
line_name : str
The name to use for the text edit
required : boolean
Whethere to display the little blue required asterix
parent : QWidget
"""
QWidget.__init__(self, parent=parent)
self.layout = QHBoxLayout()
self.qlbl = QLabel(label, self)
self.added_line = QPlainTextEdit()
max_line_height = self.added_line.fontMetrics().height() + 10
self.added_line.setMaximumHeight(max_line_height)
self.added_line.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.added_line.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.added_line.setLineWrapMode(QPlainTextEdit.NoWrap)
self.added_line.textChanged.connect(self.remove_returns)
if spellings:
self.highlighter = Highlighter(self.added_line.document())
if not placeholder_text is None:
self.added_line.setPlaceholderText(placeholder_text)
self.added_line.setObjectName(line_name)
self.layout.addWidget(self.qlbl)
self.layout.addWidget(self.added_line)
if required:
self.required_label = QLabel(self)
font = QFont()
font.setFamily("Arial")
font.setPointSize(9)
font.setBold(False)
font.setItalic(False)
font.setWeight(50)
self.required_label.setFont(font)
self.required_label.setScaledContents(True)
self.required_label.setAlignment(QtCore.Qt.AlignHCenter
| QtCore.Qt.AlignVCenter)
self.required_label.setIndent(0)
self.required_label.setText(
QtCore.QCoreApplication.translate(
"", "<html><head/><body><p align=\"center\">"
"<span style=\" font-size:18pt; color:#55aaff;\">*"
"</span></p></body></html>"))
self.layout.addWidget(self.required_label)
self.layout.setContentsMargins(1, 1, 1, 1)
self.layout.setSpacing(10)
self.setLayout(self.layout)
def remove_returns(self):
self.added_line.textChanged.disconnect()
cursor = self.added_line.textCursor()
curtext = self.added_line.toPlainText()
newtext = curtext.replace('\n', ' ')
self.added_line.setPlainText(newtext)
self.added_line.setTextCursor(cursor)
self.added_line.textChanged.connect(self.remove_returns)
def setText(self, text):
utils.set_text(self.added_line, text)
cursor = self.added_line.textCursor()
cursor.setPosition(0)
self.added_line.setTextCursor(cursor)
def text(self):
return self.added_line.toPlainText()
class WeatherInput(QWidget):
"""
Weather parameter input for GUI. Contains selector on whether to scrape, import, or ignore with corresponding
windows for each based on current selection e.g. parameter input fields if scraping.
"""
def __init__(self):
super().__init__()
self.__init_weather()
self.__init_design()
def __init_weather(self):
self.layout = QVBoxLayout()
self.__scrape()
self.__import()
self.__none()
self.__revolver()
self.__selector()
self.layout.addWidget(self.selector)
self.layout.addWidget(self.revolver)
self.layout.addWidget(QLabel("Powered by the <a href=\"https://www.weatherbit.io/\">Weatherbit API</a>"))
self.setLayout(self.layout)
def __scrape(self):
input_fields = [("City", "text"), ("State", "text"), ("Country", "text"), ("Days", "text"),
("weatherbit.io Key", "text")]
input_defaults = {"City": "Cambridge", "State": "MA", "Country": "US", "Days": "14"}
self.scrape_layout, self.scrape_fields = basic_form_creator(input_fields, input_defaults)
# adding "Imperial Units" and "Save Weather" options as checkboxes in same row.
imperial = QCheckBox("Imperial Units")
imperial.setChecked(True) # default is checked
save = QCheckBox("Save")
self.scrape_fields["Imperial Units"] = imperial
self.scrape_fields["Save Weather"] = save
self.checkbox_layout = QHBoxLayout()
self.checkbox_layout.addWidget(imperial)
self.checkbox_layout.addWidget(save)
self.checkbox_layout.addStretch()
checkbox = QWidget()
checkbox.setLayout(self.checkbox_layout)
self.scrape_layout.addWidget(checkbox)
self.scrape = QWidget(self)
self.scrape.setLayout(self.scrape_layout)
def __import(self):
self.import_layout = QVBoxLayout()
button = QPushButton("Browse")
self.import_path = QPlainTextEdit()
font_height = self.import_path.fontMetrics().height()
num_rows = 5 # size of browse window, plenty of space to display full path
self.import_path.setFixedHeight(int(num_rows * font_height))
self.import_layout.addWidget(button, 0, Qt.AlignTop | Qt.AlignLeft) # align top-left corner
self.import_layout.addWidget(self.import_path, 0, Qt.AlignTop | Qt.AlignLeft)
button.clicked.connect(lambda: self.import_path.setPlainText(QFileDialog.getOpenFileName()[0]))
self.import_ = QWidget(self)
self.import_.setLayout(self.import_layout)
def __selector(self):
self.selector_layout = QHBoxLayout()
self.selector_button_group = QButtonGroup()
self.selector_button_group.setExclusive(True)
self.none_button = QRadioButton("None")
self.scrape_button = QRadioButton("Scrape")
self.import_button = QRadioButton("Import")
self.selector_button_group.addButton(self.none_button, 1)
self.selector_button_group.addButton(self.scrape_button, 2) # need 1-index because 0 means not found
self.selector_button_group.addButton(self.import_button, 3)
self.selector_layout.addWidget(self.none_button)
self.selector_layout.addWidget(self.scrape_button)
self.selector_layout.addWidget(self.import_button)
self.selector_layout.addStretch()
self.scrape_button.setChecked(True)
self.selector = QWidget(self)
self.selector.setLayout(self.selector_layout)
def __none(self):
self.none_ = QWidget()
def __revolver(self):
self.revolver = QStackedWidget()
self.revolver.addWidget(self.none_)
self.revolver.addWidget(self.scrape)
self.revolver.addWidget(self.import_)
self.revolver.setCurrentIndex(1) # default setting is scrape
def switch_window(self, button):
"""
Switch input fields based on current selection.
:param button: radio button of current selection
:return: nothing, mutates object
"""
self.revolver.setCurrentIndex(self.selector_button_group.id(button) - 1) # make up for 1-index
def __init_design(self):
self.layout.setContentsMargins(0, 0, 0, 0)
self.layout.setSpacing(0)
self.scrape_layout.setContentsMargins(0, 3, 11, 0) # effort to line up to TwilightInput
self.scrape_layout.setSpacing(5)
self.import_layout.setSpacing(10)
self.import_layout.addStretch(1)
self.selector_layout.setContentsMargins(0, 0, 0, 11)
self.checkbox_layout.setContentsMargins(0, 0, 0, 0)
self.scrape_layout.addStretch(25) # stretch large enough to move checkboxes close to other fields
self.default_border = self.scrape_fields["City"].styleSheet() # just get from any existing line edit
self.error_border = "border: 1px solid red;"
class ScriptWriterDialog(QDialog):
def __init__(self, parent=None):
super(ScriptWriterDialog, self).__init__(parent)
self.setGeometry(200, 100, 650, 700)
font = QFontDatabase.systemFont(QFontDatabase.FixedFont)
font.setFixedPitch(True)
font.setPointSize(11)
self.editor = QPlainTextEdit()
self.editor.setFont(font)
self.editor.setPlainText(templatestr)
self.editor.setTabStopWidth(self.editor.fontMetrics().width(" ") * 4)
# access the 'text' of QPlainTextEdit by
self.highlight = ScriptHighlighter(self.editor.document())
# replace system stdout with custom object to hijack it
sys.stdout = Stream(newText=self.onUpdateText)
self.stdoutbox = QTextEdit()
self.stdoutbox.moveCursor(QTextCursor.Start)
self.stdoutbox.setFixedHeight(150)
self.loadScriptButton = QPushButton("Load script")
self.checkSpacesButton = QPushButton("Convert tabs")
self.saveScriptButton = QPushButton("Save script")
self.runScriptButton = QPushButton("Run Script")
self.buttonsLayout = QHBoxLayout()
self.buttonsLayout.addWidget(self.loadScriptButton)
self.buttonsLayout.addWidget(self.checkSpacesButton)
self.buttonsLayout.addWidget(self.saveScriptButton)
self.buttonsLayout.addWidget(self.runScriptButton)
self.layout = QVBoxLayout()
self.currentfilelabel = QLabel("No scripts loaded")
self.layout.addWidget(self.currentfilelabel)
self.layout.addWidget(self.editor)
self.layout.addLayout(self.buttonsLayout)
self.layout.addWidget(QLabel("status message:"))
self.layout.addWidget(self.stdoutbox)
self.setLayout(self.layout)
self.setWindowTitle("easyAMPS Script editor v0.1")
self.setup_button_behavior()
def setup_button_behavior(self):
self.loadScriptButton.clicked.connect(self.loadscript)
self.checkSpacesButton.clicked.connect(self.converttabs)
self.saveScriptButton.clicked.connect(self.savescript)
self.runScriptButton.clicked.connect(self.runscript)
def loadscript(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
fileName, fileType = QFileDialog.getOpenFileName(
self,
"Open AMPS yaml configuration script",
"",
"YAML file (*.yaml)",
options=options,
)
if fileName:
self.currentfilepath = Path(fileName)
self.currentfilelabel.setText(str(self.currentfilepath))
# raw text is loaded too
with open(self.currentfilepath, "rt") as fhd:
scriptbody = "".join(fhd.readlines())
self.editor.setPlainText(scriptbody)
print("Script is loaded.")
else:
return False
pass
def converttabs(self):
scriptbody = self.editor.toPlainText()
scriptbody = scriptbody.replace("\t", " ")
print("Tabs have been replaced by spaces, check the script")
# get current cursor position
cursor = self.editor.textCursor()
cursor.beginEditBlock()
# load the replaced script
self.editor.setPlainText(scriptbody)
cursor.endEditBlock()
def savescript(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
fileName, fileType = QFileDialog.getSaveFileName(
self,
"Save AMPS yaml configuration script",
"",
"YAML file (*.yaml)",
options=options,
)
if fileName:
targetfile = Path(fileName).with_suffix(".yaml")
# get text body
scriptbody = self.editor.toPlainText()
# replace tabs with spaces
scriptbody = scriptbody.replace("\t", " ")
with open(targetfile, "wt") as fhd:
fhd.write(scriptbody)
print(f"Saved to {targetfile}")
@safecall
def runscript(self):
""" Execute script from editor """
scriptbody = self.editor.toPlainText()
scriptbody = scriptbody.replace("\t", " ")
scriptconfig = yaml.load(scriptbody, Loader=yaml.FullLoader)
print("Running script ...")
inputdir = Path(scriptconfig["directories"]["input"])
outdir = Path(scriptconfig["directories"]["output"])
print(f"Reading input files from : {inputdir}")
print(f"Processed files will be saved to : {outdir}")
if not outdir.exists():
outdir.mkdir(exist_ok=True, parents=True)
experiments = {
name: Path(inputdir / filename)
for name, filename in scriptconfig["experiments"].items()
}
# load blank file
blank = read_detail(experiments["blank"])
# go through each experiment
for expt_key in experiments.keys():
if expt_key != "blank":
print(f"Experiment : {expt_key}")
if expt_key not in scriptconfig.keys():
# skip experiment that has no configurations
print(
f"Could not find configuration for '{expt_key}' experiment. Skipping it.'"
)
continue
else:
alldata = read_detail(experiments[expt_key],
label_rows=False)
timepoints = alldata["Read #"].unique().tolist()
lastread = timepoints[-1]
print(f"Found {len(timepoints)} read # :")
print(timepoints)
data = alldata
subtract_blank_fluorescence(data, blank)
datadict = process_experiment(data,
scriptconfig,
expt_key,
transpose_block=False)
for name, dataframe in datadict.items():
output_filename = f"{name}.csv"
output_target = outdir / output_filename
dataframe.to_csv(f"{str(output_target)}", index=False)
def onUpdateText(self, text):
cursor = self.stdoutbox.textCursor()
cursor.movePosition(QTextCursor.End)
cursor.insertText(text)
self.stdoutbox.setTextCursor(cursor)
self.stdoutbox.ensureCursorVisible()
def __del__(self):
sys.stdout = sys.__stdout__
