gurudesh/pytracebugs huggingface dataset:
# Buggy code
def refresh_regexp(self):
    state = RegexpState()
    regexp_text = self.__value
    self.regexp_display.StartStyling(0, 0xFF)
    self.regexp_display.SetStyling(len(regexp_text), STYLE_ERROR)
    try:
        parse(regexp_text, state)
    except:
        pass
    for i in range(state.position):
        self.regexp_display.StartStyling(i, 0xFF)
        self.regexp_display.SetStyling(1, state.token_labels[i])
    pos = self.regexp_display.CurrentPos
    if state.open_expression_start is not None:
        self.regexp_display.BraceBadLight(state.open_expression_start)
    elif (
        0 < pos < len(state.matching_braces)
        and state.matching_braces[pos - 1] is not None
    ):
        self.regexp_display.BraceHighlight(state.matching_braces[pos - 1], pos - 1)
    else:
        self.regexp_display.BraceHighlight(
            wx.stc.STC_INVALID_POSITION, wx.stc.STC_INVALID_POSITION
        )


# Traceback (wx._core.wxAssertionError)
Traceback (most recent call last):
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/module_view/_module_view.py", line 1288, in on_button_pressed
new_value = regexp_editor.edit_regexp(
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/regexp_editor.py", line 61, in edit_regexp
frame = RegexpDialog(parent, style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/regexp_editor.py", line 134, in __init__
sizer.Add(hsizer, 0, wx.GROW | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
wx._core.wxAssertionError: C++ assertion "!(flags &amp; wxALIGN_CENTRE_VERTICAL)" failed at /Users/robind/projects/bb2/dist-osx-py38/build/ext/wxWidgets/src/common/sizer.cpp(2077) in DoInsert(): Vertical alignment flags are ignored in vertical sizers

# Fixed code
def refresh_regexp(self):
    state = RegexpState()
    regexp_text = self.__value
    self.regexp_display.StartStyling(0)
    self.regexp_display.SetStyling(len(regexp_text), STYLE_ERROR)
    try:
        parse(regexp_text, state)
    except:
        pass
    for i in range(state.position):
        self.regexp_display.StartStyling(i)
        self.regexp_display.SetStyling(1, state.token_labels[i])
    pos = self.regexp_display.CurrentPos
    if state.open_expression_start is not None:
        self.regexp_display.BraceBadLight(state.open_expression_start)
    elif (
        0 < pos < len(state.matching_braces)
        and state.matching_braces[pos - 1] is not None
    ):
        self.regexp_display.BraceHighlight(state.matching_braces[pos - 1], pos - 1)
    else:
        self.regexp_display.BraceHighlight(
            wx.stc.STC_INVALID_POSITION, wx.stc.STC_INVALID_POSITION
        )
# Buggy code
def outlines(self):
    """Get a mask of all the points on the border of objects"""
    if self._outlines is None:
        for i, labels in enumerate(self.labels):
            if i == 0:
                self._outlines = centrosome.outline.outline(labels) != 0
            else:
                self._outlines |= centrosome.outline.outline(labels) != 0
        if self.line_width > 1:
            hw = float(self.line_width) / 2
            d = scipy.ndimage.distance_transform_edt(~self._outlines)
            dti, dtj = numpy.where((d < hw + 0.5) & ~self._outlines)
            self._outlines = self._outlines.astype(numpy.float32)
            self._outlines[dti, dtj] = numpy.minimum(1, hw + 0.5 - d[dti, dtj])

    return self._outlines.astype(numpy.float32)


# Traceback (AttributeError)
Traceback (most recent call last):
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 131, in <lambda>
add_object_button.Bind(wx.EVT_BUTTON, lambda event: self.add_objects_row())
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 258, in add_objects_row
self.add_row(
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 294, in add_row
self.update_menu(self.frame.menu_subplots)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 397, in update_menu
self.image.on_update_menu(event, menu)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/artist.py", line 847, in on_update_menu
if idx >= len(menu_items) or menu_items[idx].Text != label:
AttributeError: 'MenuItem' object has no attribute 'Text'

# Fixed code
def outlines(self):
    """Get a mask of all the points on the border of objects"""
    if self._outlines is None:
        for i, labels in enumerate(self.labels):
            if i == 0:
                self._outlines = centrosome.outline.outline(labels) != 0
            else:
                self._outlines |= centrosome.outline.outline(labels) != 0
        if self.line_width is not None and self.line_width > 1:
            hw = float(self.line_width) / 2
            d = scipy.ndimage.distance_transform_edt(~self._outlines)
            dti, dtj = numpy.where((d < hw + 0.5) & ~self._outlines)
            self._outlines = self._outlines.astype(numpy.float32)
            self._outlines[dti, dtj] = numpy.minimum(1, hw + 0.5 - d[dti, dtj])

    return self._outlines.astype(numpy.float32)
# Buggy code
def __init__(self, images=None, objects=None, masks=None, interpolation=None):
    """Initialize the artist with the images and objects"""
    super(CPImageArtist, self).__init__()
    self.__images = images or []
    self.__objects = objects or []
    self.__masks = masks or []
    self.__interpolation = interpolation
    self.filterrad = 4.0


# Traceback (AttributeError)
Traceback (most recent call last):
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 131, in <lambda>
add_object_button.Bind(wx.EVT_BUTTON, lambda event: self.add_objects_row())
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 258, in add_objects_row
self.add_row(
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 294, in add_row
self.update_menu(self.frame.menu_subplots)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 397, in update_menu
self.image.on_update_menu(event, menu)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/artist.py", line 847, in on_update_menu
if idx >= len(menu_items) or menu_items[idx].Text != label:
AttributeError: 'MenuItem' object has no attribute 'Text'

# Fixed code
def __init__(self, images=None, objects=None, masks=None, interpolation=None):
    """Initialize the artist with the images and objects"""
    super(CPImageArtist, self).__init__()
    self.__images = images or []
    self.__objects = objects or []
    self.__masks = masks or []
    self.__interpolation = interpolation
    self.filterrad = 0  # This was 4.0 but WHY?!?!
# Buggy code
def on_help(event):
    HTMLDialog(
        panel,
        "Workspace viewer help",
        "WORKSPACE_VIEWER_HELP",
    ).Show()


# Traceback (AttributeError)
Traceback (most recent call last):
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 131, in <lambda>
add_object_button.Bind(wx.EVT_BUTTON, lambda event: self.add_objects_row())
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 258, in add_objects_row
self.add_row(
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 294, in add_row
self.update_menu(self.frame.menu_subplots)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 397, in update_menu
self.image.on_update_menu(event, menu)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/artist.py", line 847, in on_update_menu
if idx >= len(menu_items) or menu_items[idx].Text != label:
AttributeError: 'MenuItem' object has no attribute 'Text'

# Fixed code
def on_help(event):
    HTMLDialog(
        panel,
        "Workspace viewer help",
        rst_to_html_fragment(WORKSPACE_VIEWER_HELP),
    ).Show()
# Buggy code
def scale_axes(self):
    """Set the axes limits appropriate to the images we have"""
    ax = self.image.axes
    if self.frame.navtoolbar.is_home():
        max_x = max_y = 0
        for image_row in self.image_rows:
            if image_row.data.mode != MODE_HIDE:
                shape = image_row.data.pixel_data.shape
                max_x = max(shape[1], max_x)
                max_y = max(shape[0], max_y)
        if max_x > 0 and max_y > 0:
            max_x -= 0.5
            max_y -= 0.5
            ax.set_xlim(-0.5, max_x)
            ax.set_ylim(-0.5, max_y)
            ax.invert_yaxis()
            self.__axes_scale = (max_y, max_x)
            self.frame.navtoolbar.reset()


# Traceback (AttributeError)
Traceback (most recent call last):
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 131, in <lambda>
add_object_button.Bind(wx.EVT_BUTTON, lambda event: self.add_objects_row())
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 258, in add_objects_row
self.add_row(
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 294, in add_row
self.update_menu(self.frame.menu_subplots)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 397, in update_menu
self.image.on_update_menu(event, menu)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/artist.py", line 847, in on_update_menu
if idx >= len(menu_items) or menu_items[idx].Text != label:
AttributeError: 'MenuItem' object has no attribute 'Text'

# Fixed code
def scale_axes(self):
    """Set the axes limits appropriate to the images we have"""
    max_x = max_y = 0
    for image_row in self.image_rows:
        if image_row.data.mode != MODE_HIDE:
            shape = image_row.data.pixel_data.shape
            max_x = max(shape[1], max_x)
            max_y = max(shape[0], max_y)
    if self.__axes_scale is not None:
        init_x, init_y = self.__axes_scale
        if float(max_x) != init_x[1] or float(max_y) != init_y[0]:
            self.__axes_scale = None
            self.frame.navtoolbar._nav_stack.clear()
        elif init_x != self.axes.get_xlim() or init_y != self.axes.get_ylim():
            return
    if max_x > 0 and max_y > 0:
        self.axes.set_xlim(0, max_x)
        self.axes.set_ylim(0, max_y)
        self.axes.invert_yaxis()
        self.__axes_scale = ((0.0, float(max_x)), (float(max_y), 0.0))
        self.frame.navtoolbar.reset()
# Buggy code
def remove_row(self, rows, grid_sizer, remove_button):
    for i, vw_row in enumerate(rows):
        if vw_row.remove_button == remove_button:
            break
    else:
        return
    for control in (
        vw_row.chooser,
        vw_row.color_ctrl,
        vw_row.show_check,
        vw_row.remove_button,
    ):
        grid_sizer.Remove(control)
        control.Destroy()
    self.image.remove(vw_row.data)
    rows.remove(vw_row)
    for ii in range(i, len(rows)):
        vw_row = rows[ii]
        for j, control in enumerate(
            (
                vw_row.chooser,
                vw_row.color_ctrl,
                vw_row.show_check,
                vw_row.remove_button,
            )
        ):
            grid_sizer.SetItemPosition(control, (ii + 1, j))
    self.update_menu(self.frame.menu_subplots)
    self.layout()
    self.redraw()


# Traceback (AttributeError)
Traceback (most recent call last):
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 131, in <lambda>
add_object_button.Bind(wx.EVT_BUTTON, lambda event: self.add_objects_row())
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 258, in add_objects_row
self.add_row(
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 294, in add_row
self.update_menu(self.frame.menu_subplots)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 397, in update_menu
self.image.on_update_menu(event, menu)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/artist.py", line 847, in on_update_menu
if idx >= len(menu_items) or menu_items[idx].Text != label:
AttributeError: 'MenuItem' object has no attribute 'Text'

# Fixed code
def remove_row(self, rows, grid_sizer, remove_button):
    for i, vw_row in enumerate(rows):
        if vw_row.remove_button == remove_button:
            break
    else:
        return
    for control in (
        vw_row.chooser,
        vw_row.color_ctrl,
        vw_row.show_check,
        vw_row.remove_button,
    ):
        control.Destroy()
    self.image.remove(vw_row.data)
    rows.remove(vw_row)
    for ii in range(i, len(rows)):
        vw_row = rows[ii]
        for j, control in enumerate(
            (
                vw_row.chooser,
                vw_row.color_ctrl,
                vw_row.show_check,
                vw_row.remove_button,
            )
        ):
            grid_sizer.SetItemPosition(control, (ii + 1, j))
    self.update_menu(self.frame.menu_subplots)
    self.layout()
    self.redraw()
# Buggy code
def on_choice(self, event):
    self.data.name = self.chooser.GetStringSelection()
    self.workspace_view.redraw()


# Traceback (AttributeError)
Traceback (most recent call last):
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 131, in <lambda>
add_object_button.Bind(wx.EVT_BUTTON, lambda event: self.add_objects_row())
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 258, in add_objects_row
self.add_row(
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 294, in add_row
self.update_menu(self.frame.menu_subplots)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/workspace_view/_workspace_view.py", line 397, in update_menu
self.image.on_update_menu(event, menu)
File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/artist.py", line 847, in on_update_menu
if idx >= len(menu_items) or menu_items[idx].Text != label:
AttributeError: 'MenuItem' object has no attribute 'Text'

# Fixed code
def on_choice(self, event):
    self.data.name = self.chooser.GetStringSelection()
    self.show_check.SetValue(True)
    self.workspace_view.redraw()
# Buggy code
def run_as_data_tool(self, workspace):
    """Run the module as a data tool

    ExportToDatabase has two modes - writing CSVs and writing directly.
    We write CSVs in post_run. We write directly in run.
    """
    #
    # The measurements may have been created by an old copy of CP. We
    # have to hack our measurement column cache to circumvent this.
    #
    m = workspace.measurements
    assert isinstance(m, cellprofiler_core.measurement.Measurements)
    d = self.get_dictionary()
    columns = m.get_measurement_columns()
    for i, (object_name, feature_name, coltype) in enumerate(columns):
        if (
            object_name == cellprofiler_core.measurement.IMAGE
            and feature_name.startswith(C_THUMBNAIL)
        ):
            columns[i] = (
                object_name,
                feature_name,
                cellprofiler_core.measurement.COLTYPE_LONGBLOB,
            )
    columns = self.filter_measurement_columns(columns)
    d[D_MEASUREMENT_COLUMNS] = columns

    if not self.prepare_run(workspace, as_data_tool=True):
        return
    self.prepare_group(workspace, None, None)
    if self.db_type != DB_MYSQL_CSV:
        workspace.measurements.is_first_image = True

        for i in range(workspace.measurements.image_set_count):
            if i > 0:
                workspace.measurements.next_image_set()
            self.run(workspace)
    else:
        workspace.measurements.image_set_number = workspace.measurements.image_set_count
    self.post_run(workspace)


# Traceback (AttributeError)
"Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.pyc", line 2444, in module_display_request
File "cellprofiler\modules\exporttodatabase.pyc", line 3227, in display
AttributeError: 'DisplayData' object has no attribute 'columns'"

# Fixed code
def run_as_data_tool(self, workspace):
    """Run the module as a data tool

    ExportToDatabase has two modes - writing CSVs and writing directly.
    We write CSVs in post_run. We write directly in run.
    """
    #
    # The measurements may have been created by an old copy of CP. We
    # have to hack our measurement column cache to circumvent this.
    #
    m = workspace.measurements
    assert isinstance(m, cellprofiler_core.measurement.Measurements)
    d = self.get_dictionary()
    columns = m.get_measurement_columns()
    for i, (object_name, feature_name, coltype) in enumerate(columns):
        if (
            object_name == cellprofiler_core.measurement.IMAGE
            and feature_name.startswith(C_THUMBNAIL)
        ):
            columns[i] = (
                object_name,
                feature_name,
                cellprofiler_core.measurement.COLTYPE_LONGBLOB,
            )
    columns = self.filter_measurement_columns(columns)
    d[D_MEASUREMENT_COLUMNS] = columns

    if not self.prepare_run(workspace, as_data_tool=True):
        return
    self.prepare_group(workspace, None, None)
    workspace.measurements.is_first_image = True

    for i in range(workspace.measurements.image_set_count):
        if i > 0:
            workspace.measurements.next_image_set()
        self.run(workspace)
    self.post_run(workspace)
# Buggy code
def post_run(self, workspace):
    if self.save_cpa_properties.value:
        self.write_properties_file(workspace)
    if self.create_workspace_file.value:
        self.write_workspace_file(workspace)
    if self.db_type == DB_MYSQL_CSV:
        path = self.directory.get_absolute_path(
            None if workspace is None else workspace.measurements
        )
        if not os.path.isdir(path):
            os.makedirs(path)
        self.write_mysql_table_defs(workspace)
        self.write_csv_data(workspace)
    else:
        self.write_post_run_measurements(workspace)


# Traceback (AttributeError)
"Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.pyc", line 2444, in module_display_request
File "cellprofiler\modules\exporttodatabase.pyc", line 3227, in display
AttributeError: 'DisplayData' object has no attribute 'columns'"

# Fixed code
def post_run(self, workspace):
    if self.save_cpa_properties.value:
        self.write_properties_file(workspace)
    if self.create_workspace_file.value:
        self.write_workspace_file(workspace)
    self.write_post_run_measurements(workspace)
# Buggy code
def on_debug_random_image_set(self, event):
    group_index = (
        0
        if len(self.__groupings) == 1
        else numpy.random.randint(0, len(self.__groupings) - 1, size=1)
    )
    keys, image_numbers = self.__groupings[group_index]
    if len(image_numbers) == 0:
        return
    numpy.random.seed()
    image_number_index = numpy.random.randint(1, len(image_numbers), size=1)[0]
    self.__within_group_index = (image_number_index - 1) % len(image_numbers)
    image_number = image_numbers[self.__within_group_index]
    self.__debug_measurements.next_image_set(image_number)
    self.debug_init_imageset()
    self.__debug_outlines = {}


# Traceback (ValueError)
Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.pyc", line 2969, in on_debug_random_image_set
File "mtrand.pyx", line 941, in mtrand.RandomState.randint (numpy\random\mtrand\mtrand.c:10717)
ValueError: low >= high

# Fixed code
def on_debug_random_image_set(self, event):
    keys, image_numbers = self.__groupings[self.__grouping_index]
    numpy.random.seed()
    if len(image_numbers) == 0:
        return
    elif len(image_numbers) == 1:
        self.__within_group_index = 0
    else:
        self.__within_group_index = numpy.random.randint(0, len(image_numbers))
    image_number = image_numbers[self.__within_group_index]
    self.__debug_measurements.next_image_set(image_number)
    self.debug_init_imageset()
    self.__debug_outlines = {}
# Buggy code
def on_setting_changed(self, setting, pipeline):
    if (
        setting == self.wants_groups
        and self.wants_groups
        and not self.image_sets_initialized
    ):
        workspace = self.workspace
        self.on_deactivated()
        self.on_activated(workspace)
        needs_prepare_run = False
    else:
        needs_prepare_run = True
    #
    # Unfortunately, test_valid has the side effect of getting
    # the choices set which is why it's called here
    #
    is_valid = True
    for group in self.grouping_metadata:
        try:
            group.metadata_choice.test_valid(pipeline)
        except:
            is_valid = False
    if is_valid:
        if needs_prepare_run:
            result = self.prepare_run(self.workspace)
            if not result:
                return
        self.update_tables()


# Traceback (ValueError)
Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.pyc", line 2969, in on_debug_random_image_set
File "mtrand.pyx", line 941, in mtrand.RandomState.randint (numpy\random\mtrand\mtrand.c:10717)
ValueError: low >= high

# Fixed code
def on_setting_changed(self, setting, pipeline):
    if (
        setting == self.wants_groups
        and self.wants_groups
        and not self.image_sets_initialized
    ):
        workspace = self.workspace
        self.on_deactivated()
        self.on_activated(workspace)
        needs_prepare_run = False
    else:
        needs_prepare_run = True
    #
    # Unfortunately, test_valid has the side effect of getting
    # the choices set which is why it's called here
    #
    is_valid = True
    for group in self.grouping_metadata:
        try:
            group.metadata_choice.test_valid(pipeline)
        except:
            is_valid = False
    if is_valid:
        if needs_prepare_run:
            result = self.prepare_run(self.workspace)
        self.update_tables()
# Buggy code
def debug_choose_group(self, index):
    self.__grouping_index = index
    self.__within_group_index = 0
    workspace = cellprofiler.gui.workspace.Workspace(
        self.__pipeline,
        None,
        None,
        None,
        self.__debug_measurements,
        self.__debug_image_set_list,
        self.__frame,
    )

    self.__pipeline.prepare_group(
        workspace,
        self.__groupings[self.__grouping_index][0],
        self.__groupings[self.__grouping_index][1],
    )
    key, image_numbers = self.__groupings[self.__grouping_index]
    image_number = image_numbers[self.__within_group_index]
    self.__debug_measurements.next_image_set(image_number)
    self.__pipeline_list_view.reset_debug_module()
    self.__debug_outlines = {}


# Traceback (ValueError)
Traceback (most recent call last):
File "D:\Trunk\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2813, in do_step
self.__pipeline.run_module(module, workspace)
File "D:\Trunk\CellProfiler\cellprofiler\pipeline.py", line 2059, in run_module
module.run(workspace)
File "D:\Trunk\CellProfiler\cellprofiler\modules\graytocolor.py", line 259, in run
must_be_grayscale=True)
File "D:\Trunk\CellProfiler\cellprofiler\measurements.py", line 1643, in get_image
raise ValueError("Image must be grayscale, but it was color")
ValueError: Image must be grayscale, but it was color

# Fixed code
def debug_choose_group(self, index):
    self.__grouping_index = index
    self.__within_group_index = 0
    workspace = cellprofiler.gui.workspace.Workspace(
        self.__pipeline,
        None,
        None,
        None,
        self.__debug_measurements,
        self.__debug_image_set_list,
        self.__frame,
    )

    self.__pipeline.prepare_group(
        workspace,
        self.__groupings[self.__grouping_index][0],
        self.__groupings[self.__grouping_index][1],
    )
    key, image_numbers = self.__groupings[self.__grouping_index]
    image_number = image_numbers[self.__within_group_index]
    self.__debug_measurements.next_image_set(image_number)
    self.debug_init_imageset()
    self.__debug_outlines = {}
# Buggy code
def __on_browse(self, event, edit_box, text):
    dir_dialog = wx.DirDialog(
        self.__panel, string.capitalize(text), edit_box.GetValue()
    )
    if dir_dialog.ShowModal() == wx.ID_OK:
        edit_box.SetValue(dir_dialog.GetPath())
        fake_event = wx.CommandEvent(wx.wxEVT_COMMAND_TEXT_UPDATED)
        fake_event.SetEventObject(edit_box)
        fake_event.SetId(edit_box.Id)
        edit_box.GetEventHandler().ProcessEvent(fake_event)


# Traceback (IndexError)
Traceback (most recent call last):
File "/home/emmenlau/BioDataAnalysis/Projects/TargetInfectX/CellProfiler/GIT-CellProfiler2/cellprofiler/pipeline.py", line 2359, in post_group
module.post_group(workspace, grouping)
File "/home/emmenlau/BioDataAnalysis/Projects/TargetInfectX/CellProfiler/GIT-CellProfiler2/cellprofiler/modules/trackobjects.py", line 1459, in post_group
self.recalculate_kalman_filters(workspace, image_numbers)
File "/home/emmenlau/BioDataAnalysis/Projects/TargetInfectX/CellProfiler/GIT-CellProfiler2/cellprofiler/modules/trackobjects.py", line 2886, in recalculate_kalman_filters
next_object_number[next_has_link]
IndexError: arrays used as indices must be of integer (or boolean) type

# Fixed code
def __on_browse(self, event, edit_box, text):
    dir_dialog = wx.DirDialog(self.__panel, str.capitalize(text), edit_box.GetValue())
    if dir_dialog.ShowModal() == wx.ID_OK:
        edit_box.SetValue(dir_dialog.GetPath())
        fake_event = wx.CommandEvent(wx.wxEVT_COMMAND_TEXT_UPDATED)
        fake_event.SetEventObject(edit_box)
        fake_event.SetId(edit_box.Id)
        edit_box.GetEventHandler().ProcessEvent(fake_event)
# Buggy code
def open_csv(self, do_not_cache=False):
    """Open the csv file or URL, returning a file descriptor"""
    global header_cache

    if cellprofiler.preferences.is_url_path(self.csv_path):
        if self.csv_path not in header_cache:
            header_cache[self.csv_path] = {}
        entry = header_cache[self.csv_path]
        if "URLEXCEPTION" in entry:
            raise entry["URLEXCEPTION"]
        if "URLDATA" in entry:
            fd = StringIO(entry["URLDATA"])
        else:
            if do_not_cache:
                raise RuntimeError("Need to fetch URL manually.")
            try:
                url = cellprofiler.misc.generate_presigned_url(self.csv_path)
                url_fd = six.moves.urllib.request.urlopen(url)
            except Exception as e:
                entry["URLEXCEPTION"] = e
                raise e
            fd = StringIO()
            while True:
                text = url_fd.read()
                if len(text) == 0:
                    break
                fd.write(text)
            fd.seek(0)
            entry["URLDATA"] = fd.getvalue()
        return fd
    else:
        return open(self.csv_path, "rb")


# Traceback (IndexError)
Traceback (most recent call last):
File "/home/emmenlau/BioDataAnalysis/Projects/TargetInfectX/CellProfiler/GIT-CellProfiler2/cellprofiler/pipeline.py", line 2359, in post_group
module.post_group(workspace, grouping)
File "/home/emmenlau/BioDataAnalysis/Projects/TargetInfectX/CellProfiler/GIT-CellProfiler2/cellprofiler/modules/trackobjects.py", line 1459, in post_group
self.recalculate_kalman_filters(workspace, image_numbers)
File "/home/emmenlau/BioDataAnalysis/Projects/TargetInfectX/CellProfiler/GIT-CellProfiler2/cellprofiler/modules/trackobjects.py", line 2886, in recalculate_kalman_filters
next_object_number[next_has_link]
IndexError: arrays used as indices must be of integer (or boolean) type

# Fixed code
def open_csv(self, do_not_cache=False):
    """Open the csv file or URL, returning a file descriptor"""
    global header_cache

    if cellprofiler.preferences.is_url_path(self.csv_path):
        if self.csv_path not in header_cache:
            header_cache[self.csv_path] = {}
        entry = header_cache[self.csv_path]
        if "URLEXCEPTION" in entry:
            raise entry["URLEXCEPTION"]
        if "URLDATA" in entry:
            fd = StringIO(entry["URLDATA"])
        else:
            if do_not_cache:
                raise RuntimeError("Need to fetch URL manually.")
            try:
                url = cellprofiler.misc.generate_presigned_url(self.csv_path)
                url_fd = six.moves.urllib.request.urlopen(url)
            except Exception as e:
                entry["URLEXCEPTION"] = e
                raise e
            fd = StringIO()
            while True:
                text = url_fd.read()
                if len(text) == 0:
                    break
                fd.write(text)
            fd.seek(0)
            entry["URLDATA"] = fd.getvalue()
        return fd
    else:
        return open(self.csv_path, "rt")
# Buggy code
def enhance_dark_holes(self, image, min_radius, max_radius):
    pixel_data = image.pixel_data

    mask = image.mask if image.has_mask else None

    se = self.__structuring_element(1, image.volumetric)

    inverted_image = pixel_data.max() - pixel_data

    previous_reconstructed_image = inverted_image

    eroded_image = inverted_image

    smoothed_image = numpy.zeros(pixel_data.shape)

    for i in range(max_radius + 1):
        eroded_image = skimage.morphology.erosion(eroded_image, se)

        if mask:
            eroded_image *= mask

        reconstructed_image = skimage.morphology.reconstruction(
            eroded_image, inverted_image, "dilation", se
        )

        output_image = previous_reconstructed_image - reconstructed_image

        if i >= min_radius:
            smoothed_image = numpy.maximum(smoothed_image, output_image)

        previous_reconstructed_image = reconstructed_image

    return smoothed_image


# Traceback (ValueError)
Failed to run module EnhanceOrSuppressFeatures
Traceback (most recent call last):
File "/home/mattb/git/CellProfiler/cellprofiler/gui/pipelinecontroller.py", line 2887, in do_step
self.__pipeline.run_module(module, workspace)
File "/home/mattb/git/CellProfiler/cellprofiler/pipeline.py", line 2022, in run_module
module.run(workspace)
File "/home/mattb/git/CellProfiler/cellprofiler/modules/enhanceorsuppressfeatures.py", line 376, in run
result = self.enhance_dark_holes(image, min_radius, max_radius)
File "/home/mattb/git/CellProfiler/cellprofiler/modules/enhanceorsuppressfeatures.py", line 534, in enhance_dark_holes
if mask:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

# Fixed code
def enhance_dark_holes(self, image, min_radius, max_radius):
    pixel_data = image.pixel_data

    mask = image.mask if image.has_mask else None

    se = self.__structuring_element(1, image.volumetric)

    inverted_image = pixel_data.max() - pixel_data

    previous_reconstructed_image = inverted_image

    eroded_image = inverted_image

    smoothed_image = numpy.zeros(pixel_data.shape)

    for i in range(max_radius + 1):
        eroded_image = skimage.morphology.erosion(eroded_image, se)

        if mask is not None:
            eroded_image *= mask

        reconstructed_image = skimage.morphology.reconstruction(
            eroded_image, inverted_image, "dilation", se
        )

        output_image = previous_reconstructed_image - reconstructed_image

        if i >= min_radius:
            smoothed_image = numpy.maximum(smoothed_image, output_image)

        previous_reconstructed_image = reconstructed_image

    return smoothed_image
# Buggy code
def display_combine(self, workspace, figure):
    import matplotlib.cm

    input_image = workspace.display_data.input_image
    output_image = workspace.display_data.output_image
    figure.set_subplots((1, 2))
    figure.subplot_imshow(
        0, 0, input_image, title="Original image: %s" % self.image_name
    )
    figure.subplot_imshow(
        0,
        1,
        output_image,
        title="Grayscale image: %s" % self.grayscale_name,
        colormap=matplotlib.cm.Greys_r,
        sharexy=figure.subplot(0, 0),
    )


# Traceback (TypeError)
Failed to run module ColorToGray
Traceback (most recent call last):
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2906, in do_step
module.display(workspace, fig)
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\modules\colortogray.py", line 316, in display
self.display_split(workspace, figure)
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\modules\colortogray.py", line 379, in display_split
title="Original image")
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\gui\figure.py", line 216, in wrapper
return fn(*args, **kwargs)
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\gui\figure.py", line 1302, in subplot_imshow
subplot.imshow(self.normalize_image(image, **kwargs))
File "C:\Python27\lib\site-packages\matplotlib\__init__.py", line 1819, in inner
return func(ax, *args, **kwargs)
File "C:\Python27\lib\site-packages\matplotlib\axes\_axes.py", line 4922, in imshow
im.set_data(X)
File "C:\Python27\lib\site-packages\matplotlib\image.py", line 453, in set_data
raise TypeError("Invalid dimensions for image data")
TypeError: Invalid dimensions for image data

# Fixed code
def display_combine(self, workspace, figure):
    import matplotlib.cm

    input_image = workspace.display_data.input_image
    output_image = workspace.display_data.output_image
    figure.set_subplots((1, 2))
    figure.subplot_imshow_color(
        0, 0, input_image, title="Original image: %s" % self.image_name
    )
    figure.subplot_imshow(
        0,
        1,
        output_image,
        title="Grayscale image: %s" % self.grayscale_name,
        colormap=matplotlib.cm.Greys_r,
        sharexy=figure.subplot(0, 0),
    )
# Buggy code
def display_split(self, workspace, figure):
    import matplotlib.cm

    input_image = workspace.display_data.input_image
    disp_collection = workspace.display_data.disp_collection
    ndisp = len(disp_collection)
    ncols = int(np.ceil((ndisp + 1) ** 0.5))
    subplots = (ncols, (ndisp / ncols) + 1)
    figure.set_subplots(subplots)
    figure.subplot_imshow(0, 0, input_image, title="Original image")

    for eachplot in range(ndisp):
        placenum = eachplot + 1
        figure.subplot_imshow(
            placenum % ncols,
            placenum / ncols,
            disp_collection[eachplot][0],
            title="%s" % (disp_collection[eachplot][1]),
            colormap=matplotlib.cm.Greys_r,
            sharexy=figure.subplot(0, 0),
        )


# Traceback (TypeError)
Failed to run module ColorToGray
Traceback (most recent call last):
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2906, in do_step
module.display(workspace, fig)
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\modules\colortogray.py", line 316, in display
self.display_split(workspace, figure)
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\modules\colortogray.py", line 379, in display_split
title="Original image")
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\gui\figure.py", line 216, in wrapper
return fn(*args, **kwargs)
File "C:\Users\bcimini\GitHub\Fork\CellProfiler\cellprofiler\gui\figure.py", line 1302, in subplot_imshow
subplot.imshow(self.normalize_image(image, **kwargs))
File "C:\Python27\lib\site-packages\matplotlib\__init__.py", line 1819, in inner
return func(ax, *args, **kwargs)
File "C:\Python27\lib\site-packages\matplotlib\axes\_axes.py", line 4922, in imshow
im.set_data(X)
File "C:\Python27\lib\site-packages\matplotlib\image.py", line 453, in set_data
raise TypeError("Invalid dimensions for image data")
TypeError: Invalid dimensions for image data

# Fixed code
def display_split(self, workspace, figure):
    import matplotlib.cm

    input_image = workspace.display_data.input_image
    disp_collection = workspace.display_data.disp_collection
    ndisp = len(disp_collection)
    ncols = int(np.ceil((ndisp + 1) ** 0.5))
    subplots = (ncols, (ndisp / ncols) + 1)
    figure.set_subplots(subplots)
    figure.subplot_imshow_color(0, 0, input_image, title="Original image")

    for eachplot in range(ndisp):
        placenum = eachplot + 1
        figure.subplot_imshow(
            placenum % ncols,
            placenum / ncols,
            disp_collection[eachplot][0],
            title="%s" % (disp_collection[eachplot][1]),
            colormap=matplotlib.cm.Greys_r,
            sharexy=figure.subplot(0, 0),
        )
# Buggy code
def get_measurement_columns(self, pipeline):
    """Return information on the measurements made during cropping"""
    return [
        (cpmeas.IMAGE, x % self.cropped_image_name.value, cpmeas.COLTYPE_INTEGER)
        for x in (FF_AREA_RETAINED, FF_ORIGINAL_AREA)
    ]


# Traceback (TypeError)
Failed to run module Crop
Traceback (most recent call last):
File "CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2887, in do_step
File "CellProfiler\cellprofiler\pipeline.py", line 2022, in run_module
File "CellProfiler\cellprofiler\modules\crop.py", line 335, in run
File "CellProfiler\cellprofiler\modules\crop.py", line 437, in ui_crop
File "CellProfiler\cellprofiler\modules\crop.py", line 795, in apply_rectangle_cropping
TypeError: slice indices must be integers or None or have an __index__ method

# Fixed code
def get_measurement_columns(self, pipeline):
    """Return information on the measurements made during cropping"""
    return [
        (
            cellprofiler.measurement.IMAGE,
            x % self.cropped_image_name.value,
            cellprofiler.measurement.COLTYPE_INTEGER,
        )
        for x in (FF_AREA_RETAINED, FF_ORIGINAL_AREA)
    ]
# Buggy code
def ui_crop(self, workspace, orig_image):
    """Crop into a rectangle or ellipse, guided by UI"""
    d = self.get_dictionary(workspace.image_set_list)
    if (not d.has_key(self.shape.value)) or self.individual_or_once == IO_INDIVIDUALLY:
        d[self.shape.value] = workspace.interaction_request(
            self, d.get(self.shape.value, None), orig_image.pixel_data
        )
    if self.shape == SH_ELLIPSE:
        return self.apply_ellipse_cropping(workspace, orig_image)
    else:
        return self.apply_rectangle_cropping(workspace, orig_image)


# Traceback (TypeError)
Failed to run module Crop
Traceback (most recent call last):
File "CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2887, in do_step
File "CellProfiler\cellprofiler\pipeline.py", line 2022, in run_module
File "CellProfiler\cellprofiler\modules\crop.py", line 335, in run
File "CellProfiler\cellprofiler\modules\crop.py", line 437, in ui_crop
File "CellProfiler\cellprofiler\modules\crop.py", line 795, in apply_rectangle_cropping
TypeError: slice indices must be integers or None or have an __index__ method

# Fixed code
def ui_crop(self, workspace, orig_image):
    """Crop into a rectangle or ellipse, guided by UI"""
    d = self.get_dictionary(workspace.image_set_list)
    if (self.shape.value not in d) or self.individual_or_once == IO_INDIVIDUALLY:
        d[self.shape.value] = workspace.interaction_request(
            self, d.get(self.shape.value, None), orig_image.pixel_data
        )
    if self.shape == SH_ELLIPSE:
        return self.apply_ellipse_cropping(workspace, orig_image)
    else:
        return self.apply_rectangle_cropping(workspace, orig_image)
# Buggy code
def data_xy(mouse_event):
    """Return the mouse event's x & y converted into data-relative coords"""
    x = mouse_event.xdata
    y = mouse_event.ydata
    return x, y


# Traceback (TypeError)
Failed to run module Crop
Traceback (most recent call last):
File "CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2887, in do_step
File "CellProfiler\cellprofiler\pipeline.py", line 2022, in run_module
File "CellProfiler\cellprofiler\modules\crop.py", line 335, in run
File "CellProfiler\cellprofiler\modules\crop.py", line 437, in ui_crop
File "CellProfiler\cellprofiler\modules\crop.py", line 795, in apply_rectangle_cropping
TypeError: slice indices must be integers or None or have an __index__ method

# Fixed code
def data_xy(mouse_event):
    """Return the mouse event's x & y converted into data-relative coords"""
    x = mouse_event.xdata
    y = mouse_event.ydata
    return x, y
# Buggy code
def __init__(self, center, radius):
    """Draw an ellipse with control points at the ellipse center and
    a given x and y radius"""
    self.center_x, self.center_y = center
    self.radius_x = self.center_x + radius[0] / 2
    self.radius_y = self.center_y + radius[1] / 2
    color = cpprefs.get_primary_outline_color()
    color = np.hstack((color, [255])).astype(float) / 255.0
    self.ellipse = M.patches.Ellipse(
        center, self.width, self.height, edgecolor=color, facecolor="none"
    )
    self.center_handle = handle(self.center_x, self.center_y, self.move_center)
    self.radius_handle = handle(self.radius_x, self.radius_y, self.move_radius)


# Traceback (TypeError)
Failed to run module Crop
Traceback (most recent call last):
File "CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2887, in do_step
File "CellProfiler\cellprofiler\pipeline.py", line 2022, in run_module
File "CellProfiler\cellprofiler\modules\crop.py", line 335, in run
File "CellProfiler\cellprofiler\modules\crop.py", line 437, in ui_crop
File "CellProfiler\cellprofiler\modules\crop.py", line 795, in apply_rectangle_cropping
TypeError: slice indices must be integers or None or have an __index__ method

# Fixed code
def __init__(self, center, radius):
    """Draw an ellipse with control points at the ellipse center and
    a given x and y radius"""
    self.center_x, self.center_y = center
    self.radius_x = self.center_x + radius[0] / 2
    self.radius_y = self.center_y + radius[1] / 2
    color = cellprofiler.preferences.get_primary_outline_color()
    color = numpy.hstack((color, [255])).astype(float) / 255.0
    self.ellipse = matplotlib.patches.Ellipse(
        center, self.width, self.height, edgecolor=color, facecolor="none"
    )
    self.center_handle = Handle(self.center_x, self.center_y, self.move_center)
    self.radius_handle = Handle(self.radius_x, self.radius_y, self.move_radius)
# Buggy code
def center_x(self):
    """The handle's notion of its x coordinate"""
    return self.get_x() + self.get_width() / 2


# Traceback (TypeError)
Failed to run module Crop
Traceback (most recent call last):
File "CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2887, in do_step
File "CellProfiler\cellprofiler\pipeline.py", line 2022, in run_module
File "CellProfiler\cellprofiler\modules\crop.py", line 335, in run
File "CellProfiler\cellprofiler\modules\crop.py", line 437, in ui_crop
File "CellProfiler\cellprofiler\modules\crop.py", line 795, in apply_rectangle_cropping
TypeError: slice indices must be integers or None or have an __index__ method

# Fixed code
def center_x(self):
    """The handle's notion of its x coordinate"""
    return self.get_x() + self.get_width() / 2
# Buggy code
def center_y(self):
    """The handle's notion of its y coordinate"""
    return self.get_y() + self.get_height() / 2


# Traceback (TypeError)
Failed to run module Crop
Traceback (most recent call last):
File "CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2887, in do_step
File "CellProfiler\cellprofiler\pipeline.py", line 2022, in run_module
File "CellProfiler\cellprofiler\modules\crop.py", line 335, in run
File "CellProfiler\cellprofiler\modules\crop.py", line 437, in ui_crop
File "CellProfiler\cellprofiler\modules\crop.py", line 795, in apply_rectangle_cropping
TypeError: slice indices must be integers or None or have an __index__ method

# Fixed code
def center_y(self):
    """The handle's notion of its y coordinate"""
    return self.get_y() + self.get_height() / 2
# Buggy code
def apply_ellipse_cropping(self, workspace, orig_image):
    d = self.get_dictionary(workspace.image_set_list)
    ellipse = d[SH_ELLIPSE]
    x_center, y_center, x_radius, y_radius = [
        ellipse[x] for x in (EL_XCENTER, EL_YCENTER, EL_XRADIUS, EL_YRADIUS)
    ]
    pixel_data = orig_image.pixel_data
    x_max = pixel_data.shape[1]
    y_max = pixel_data.shape[0]
    if x_radius > y_radius:
        dist_x = math.sqrt(x_radius**2 - y_radius**2)
        dist_y = 0
        major_radius = x_radius
    else:
        dist_x = 0
        dist_y = math.sqrt(y_radius**2 - x_radius**2)
        major_radius = y_radius

    focus_1_x, focus_1_y = (x_center - dist_x, y_center - dist_y)
    focus_2_x, focus_2_y = (x_center + dist_x, y_center + dist_y)
    y, x = np.mgrid[0:y_max, 0:x_max]
    d1 = np.sqrt((x - focus_1_x) ** 2 + (y - focus_1_y) ** 2)
    d2 = np.sqrt((x - focus_2_x) ** 2 + (y - focus_2_y) ** 2)
    cropping = d1 + d2 <= major_radius * 2
    return cropping


# Traceback (TypeError)
Failed to run module Crop
Traceback (most recent call last):
File "CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2887, in do_step
File "CellProfiler\cellprofiler\pipeline.py", line 2022, in run_module
File "CellProfiler\cellprofiler\modules\crop.py", line 335, in run
File "CellProfiler\cellprofiler\modules\crop.py", line 437, in ui_crop
File "CellProfiler\cellprofiler\modules\crop.py", line 795, in apply_rectangle_cropping
TypeError: slice indices must be integers or None or have an __index__ method

# Fixed code
def apply_ellipse_cropping(self, workspace, orig_image):
    d = self.get_dictionary(workspace.image_set_list)
    ellipse = d[SH_ELLIPSE]
    x_center, y_center, x_radius, y_radius = [
        ellipse[x] for x in (EL_XCENTER, EL_YCENTER, EL_XRADIUS, EL_YRADIUS)
    ]
    pixel_data = orig_image.pixel_data
    x_max = pixel_data.shape[1]
    y_max = pixel_data.shape[0]
    if x_radius > y_radius:
        dist_x = math.sqrt(x_radius**2 - y_radius**2)
        dist_y = 0
        major_radius = x_radius
    else:
        dist_x = 0
        dist_y = math.sqrt(y_radius**2 - x_radius**2)
        major_radius = y_radius

    focus_1_x, focus_1_y = (x_center - dist_x, y_center - dist_y)
    focus_2_x, focus_2_y = (x_center + dist_x, y_center + dist_y)
    y, x = numpy.mgrid[0:y_max, 0:x_max]
    d1 = numpy.sqrt((x - focus_1_x) ** 2 + (y - focus_1_y) ** 2)
    d2 = numpy.sqrt((x - focus_2_x) ** 2 + (y - focus_2_y) ** 2)
    cropping = d1 + d2 <= major_radius * 2
    return cropping