gurudesh/pytracebugs huggingface dataset:
# Buggy code
def get_rectangle_cropping(self, workspace, orig_image):
    """Crop into a rectangle using user-specified coordinates"""
    cropping = np.ones(orig_image.pixel_data.shape[:2], bool)
    if not self.horizontal_limits.unbounded_min:
        cropping[:, : self.horizontal_limits.min] = False
    if not self.horizontal_limits.unbounded_max:
        cropping[:, self.horizontal_limits.max :] = False
    if not self.vertical_limits.unbounded_min:
        cropping[: self.vertical_limits.min, :] = False
    if not self.vertical_limits.unbounded_max:
        cropping[self.vertical_limits.max :, :] = False
    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 get_rectangle_cropping(self, workspace, orig_image):
    """Crop into a rectangle using user-specified coordinates"""
    cropping = numpy.ones(orig_image.pixel_data.shape[:2], bool)
    if not self.horizontal_limits.unbounded_min:
        cropping[:, : self.horizontal_limits.min] = False
    if not self.horizontal_limits.unbounded_max:
        cropping[:, self.horizontal_limits.max :] = False
    if not self.vertical_limits.unbounded_min:
        cropping[: self.vertical_limits.min, :] = False
    if not self.vertical_limits.unbounded_max:
        cropping[self.vertical_limits.max :, :] = False
    return cropping
# Buggy code
def apply_rectangle_cropping(self, workspace, orig_image):
    cropping = np.ones(orig_image.pixel_data.shape[:2], bool)
    d = self.get_dictionary(workspace.image_set_list)
    r = d[SH_RECTANGLE]
    left, top, right, bottom = [r[x] for x in (RE_LEFT, RE_TOP, RE_RIGHT, RE_BOTTOM)]
    if left > 0:
        cropping[:, :left] = False
    if right < cropping.shape[1]:
        cropping[:, right:] = False
    if top > 0:
        cropping[:top, :] = False
    if bottom < cropping.shape[0]:
        cropping[bottom:, :] = False
    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_rectangle_cropping(self, workspace, orig_image):
    cropping = numpy.ones(orig_image.pixel_data.shape[:2], bool)
    d = self.get_dictionary(workspace.image_set_list)
    r = d[SH_RECTANGLE]
    left, top, right, bottom = [
        int(numpy.round(r[x])) for x in (RE_LEFT, RE_TOP, RE_RIGHT, RE_BOTTOM)
    ]
    if left > 0:
        cropping[:, :left] = False
    if right < cropping.shape[1]:
        cropping[:, right:] = False
    if top > 0:
        cropping[:top, :] = False
    if bottom < cropping.shape[0]:
        cropping[bottom:, :] = False
    return cropping
# Buggy code
def print_help(event, module_name, help_text):
    """Print the help text for a module"""
    printer = wx.html.HtmlEasyPrinting(
        "Printing %s" % module_name, event.GetEventObject()
    )
    printer.GetPrintData().SetPaperId(wx.PAPER_LETTER)
    printer.PrintText(help_text)


# Traceback (TypeError)
Traceback (most recent call last):
File "cellprofiler\gui\cpframe.pyc", line 1144, in on_print
File "cellprofiler\gui\cpframe.pyc", line 1203, in print_help
File "wx\html.pyc", line 1333, in __init__
TypeError: in method 'new_HtmlEasyPrinting', expected argument 2 of type 'wxWindow *'

# Fixed code
def print_help(event, module_name, help_text):
    """Print the help text for a module"""
    printer = wx.html.HtmlEasyPrinting("Printing %s" % module_name)
    printer.GetPrintData().SetPaperId(wx.PAPER_LETTER)
    printer.PrintText(help_text)
# Buggy code
def save_help(event, module_name, help_text):
    """Save the help text for a module"""
    save_dlg = wx.FileDialog(
        event.GetEventObject(),
        message="Save help for %s to file" % module_name,
        defaultFile="%s.html" % module_name,
        wildcard="*.html",
        style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
    )
    result = save_dlg.ShowModal()
    if result == wx.ID_OK:
        pathname = save_dlg.GetPath()
        fd = open(pathname, "wt")
        fd.write(help_text)
        fd.close()


# Traceback (TypeError)
Traceback (most recent call last):
File "cellprofiler\gui\cpframe.pyc", line 1144, in on_print
File "cellprofiler\gui\cpframe.pyc", line 1203, in print_help
File "wx\html.pyc", line 1333, in __init__
TypeError: in method 'new_HtmlEasyPrinting', expected argument 2 of type 'wxWindow *'

# Fixed code
def save_help(event, module_name, help_text):
    """Save the help text for a module"""
    save_dlg = wx.FileDialog(
        event.GetEventObject().GetWindow(),
        message="Save help for %s to file" % module_name,
        defaultFile="%s.html" % module_name,
        wildcard="*.html",
        style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
    )

    result = save_dlg.ShowModal()

    if result == wx.ID_OK:
        with codecs.open(save_dlg.GetPath(), "w", encoding="utf-8") as fd:
            fd.write(
                '<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />'
            )
            fd.write(help_text)
# Buggy code
def help_settings(self):
    help_settings = [self.x_name, self.y_name, self.method, self.image_name]

    help_settings += self.apply_threshold.help_settings()[2:]

    help_settings += [
        self.distance_to_dilate,
        self.regularization_factor,
        self.fill_holes,
        self.wants_discard_edge,
        self.wants_discard_primary,
        self.new_primary_objects_name,
        self.wants_primary_outlines,
        self.new_primary_outlines_name,
        self.use_outlines,
        self.outlines_name,
    ]


# Traceback (TypeError)
Traceback (most recent call last):
File "I:\GitHub\CellProfiler\cellprofiler\gui\addmoduleframe.py", line 196, in __on_search_help
html = cellprofiler.gui.html.manual.search_module_help(self.search_text.Value)
File "I:\GitHub\CellProfiler\cellprofiler\gui\html\manual.py", line 232, in search_module_help
help_text = module.get_help()
File "I:\GitHub\CellProfiler\cellprofiler\module.py", line 227, in get_help
for setting in self.help_settings():
TypeError: 'NoneType' object is not iterable

# Fixed code
def help_settings(self):
    help_settings = [self.x_name, self.y_name, self.method, self.image_name]

    help_settings += self.apply_threshold.help_settings()[2:]

    help_settings += [
        self.distance_to_dilate,
        self.regularization_factor,
        self.fill_holes,
        self.wants_discard_edge,
        self.wants_discard_primary,
        self.new_primary_objects_name,
        self.wants_primary_outlines,
        self.new_primary_outlines_name,
        self.use_outlines,
        self.outlines_name,
    ]

    return help_settings
# Buggy code
def settings(self):
    settings = [
        self.sub_object_name,
        self.parent_name,
        self.find_parent_child_distances,
        self.wants_per_parent_means,
        self.wants_step_parent_distances,
    ]

    settings += [group.step_parent_name for group in self.step_parent_names]

    return settings


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def settings(self):
    settings = super(RelateObjects, self).settings()

    settings += [
        self.find_parent_child_distances,
        self.wants_per_parent_means,
        self.wants_step_parent_distances,
    ]

    settings += [group.step_parent_name for group in self.step_parent_names]

    return settings
# Buggy code
def visible_settings(self):
    visible_settings = [
        self.sub_object_name,
        self.parent_name,
        self.wants_per_parent_means,
        self.find_parent_child_distances,
    ]

    if self.find_parent_child_distances != D_NONE and self.has_step_parents:
        visible_settings += [self.wants_step_parent_distances]

        if self.wants_step_parent_distances:
            for group in self.step_parent_names:
                visible_settings += group.visible_settings()

            visible_settings += [self.add_step_parent_button]

    return visible_settings


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def visible_settings(self):
    visible_settings = super(RelateObjects, self).visible_settings()

    visible_settings += [self.wants_per_parent_means, self.find_parent_child_distances]

    if self.find_parent_child_distances != D_NONE and self.has_step_parents:
        visible_settings += [self.wants_step_parent_distances]

        if self.wants_step_parent_distances:
            for group in self.step_parent_names:
                visible_settings += group.visible_settings()

            visible_settings += [self.add_step_parent_button]

    return visible_settings
# Buggy code
def get_parent_names(self):
    parent_names = [self.parent_name.value]

    if self.wants_step_parent_distances.value:
        parent_names += [
            group.step_parent_name.value for group in self.step_parent_names
        ]

    return parent_names


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def get_parent_names(self):
    parent_names = [self.x_name.value]

    if self.wants_step_parent_distances.value:
        parent_names += [
            group.step_parent_name.value for group in self.step_parent_names
        ]

    return parent_names
# Buggy code
def get_child_columns(self, pipeline):
    child_columns = list(
        filter(
            lambda column: column[0] == self.sub_object_name.value
            and self.should_aggregate_feature(column[1]),
            pipeline.get_measurement_columns(self),
        )
    )

    child_columns += self.get_child_measurement_columns(pipeline)

    return child_columns


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def get_child_columns(self, pipeline):
    child_columns = list(
        filter(
            lambda column: column[0] == self.y_name.value
            and self.should_aggregate_feature(column[1]),
            pipeline.get_measurement_columns(self),
        )
    )

    child_columns += self.get_child_measurement_columns(pipeline)

    return child_columns
# Buggy code
def get_child_measurement_columns(self, pipeline):
    columns = []
    if self.find_parent_child_distances in (D_BOTH, D_CENTROID):
        for parent_name in self.get_parent_names():
            columns += [
                (
                    self.sub_object_name.value,
                    FF_CENTROID % parent_name,
                    cellprofiler.measurement.COLTYPE_INTEGER,
                )
            ]

    if self.find_parent_child_distances in (D_BOTH, D_MINIMUM):
        for parent_name in self.get_parent_names():
            columns += [
                (
                    self.sub_object_name.value,
                    FF_MINIMUM % parent_name,
                    cellprofiler.measurement.COLTYPE_INTEGER,
                )
            ]

    return columns


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def get_child_measurement_columns(self, pipeline):
    columns = []
    if self.find_parent_child_distances in (D_BOTH, D_CENTROID):
        for parent_name in self.get_parent_names():
            columns += [
                (
                    self.y_name.value,
                    FF_CENTROID % parent_name,
                    cellprofiler.measurement.COLTYPE_INTEGER,
                )
            ]

    if self.find_parent_child_distances in (D_BOTH, D_MINIMUM):
        for parent_name in self.get_parent_names():
            columns += [
                (
                    self.y_name.value,
                    FF_MINIMUM % parent_name,
                    cellprofiler.measurement.COLTYPE_INTEGER,
                )
            ]

    return columns
# Buggy code
def get_measurement_columns(self, pipeline):
    """Return the column definitions for this module's measurements"""
    columns = [
        (
            self.sub_object_name.value,
            cellprofiler.measurement.FF_PARENT % self.parent_name.value,
            cellprofiler.measurement.COLTYPE_INTEGER,
        ),
        (
            self.parent_name.value,
            cellprofiler.measurement.FF_CHILDREN_COUNT % self.sub_object_name.value,
            cellprofiler.measurement.COLTYPE_INTEGER,
        ),
    ]

    if self.wants_per_parent_means.value:
        child_columns = self.get_child_columns(pipeline)

        columns += [
            (
                self.parent_name.value,
                FF_MEAN % (self.sub_object_name.value, column[1]),
                cellprofiler.measurement.COLTYPE_FLOAT,
            )
            for column in child_columns
        ]

    columns += self.get_child_measurement_columns(pipeline)

    return columns


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def get_measurement_columns(self, pipeline):
    """Return the column definitions for this module's measurements"""
    columns = [
        (
            self.y_name.value,
            cellprofiler.measurement.FF_PARENT % self.x_name.value,
            cellprofiler.measurement.COLTYPE_INTEGER,
        ),
        (
            self.x_name.value,
            cellprofiler.measurement.FF_CHILDREN_COUNT % self.y_name.value,
            cellprofiler.measurement.COLTYPE_INTEGER,
        ),
    ]

    if self.wants_per_parent_means.value:
        child_columns = self.get_child_columns(pipeline)

        columns += [
            (
                self.x_name.value,
                FF_MEAN % (self.y_name.value, column[1]),
                cellprofiler.measurement.COLTYPE_FLOAT,
            )
            for column in child_columns
        ]

    columns += self.get_child_measurement_columns(pipeline)

    return columns
# Buggy code
def get_object_relationships(self, pipeline):
    """Return the object relationships produced by this module"""
    parent_name = self.parent_name.value

    sub_object_name = self.sub_object_name.value

    return [
        (
            cellprofiler.measurement.R_PARENT,
            parent_name,
            sub_object_name,
            cellprofiler.measurement.MCA_AVAILABLE_EACH_CYCLE,
        ),
        (
            cellprofiler.measurement.R_CHILD,
            sub_object_name,
            parent_name,
            cellprofiler.measurement.MCA_AVAILABLE_EACH_CYCLE,
        ),
    ]


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def get_object_relationships(self, pipeline):
    """Return the object relationships produced by this module"""
    parent_name = self.x_name.value

    sub_object_name = self.y_name.value

    return [
        (
            cellprofiler.measurement.R_PARENT,
            parent_name,
            sub_object_name,
            cellprofiler.measurement.MCA_AVAILABLE_EACH_CYCLE,
        ),
        (
            cellprofiler.measurement.R_CHILD,
            sub_object_name,
            parent_name,
            cellprofiler.measurement.MCA_AVAILABLE_EACH_CYCLE,
        ),
    ]
# Buggy code
def get_categories(self, pipeline, object_name):
    if object_name == self.parent_name.value:
        if self.wants_per_parent_means:
            return ["Mean_{}".format(self.sub_object_name), "Children"]
        else:
            return ["Children"]
    elif object_name == self.sub_object_name.value:
        result = ["Parent"]

        if self.find_parent_child_distances != D_NONE:
            result += [C_DISTANCE]

        return result

    return []


# Traceback (ValueError)
Traceback (most recent call last):
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2844, in do_step
self.__pipeline.run_module(module, workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\pipeline.py", line 2108, in run_module
module.run(workspace)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 252, in run
self.calculate_centroid_distances(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 336, in calculate_centroid_distances
parents_of = self.get_parents_of(workspace, parent_name)
File "C:\Users\brayma2\Desktop\GitHub\CellProfiler\cellprofiler\modules\relateobjects.py", line 475, in get_parents_of
reverse_lookup_len = max(np.max(primary_parents_of) + 1,
File "C:\Python27\lib\site-packages\numpy\core\fromnumeric.py", line 2263, in amax
out=out, keepdims=keepdims)
File "C:\Python27\lib\site-packages\numpy\core\_methods.py", line 26, in _amax
return umr_maximum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation maximum which has no identity

# Fixed code
def get_categories(self, pipeline, object_name):
    if object_name == self.x_name.value:
        if self.wants_per_parent_means:
            return ["Mean_{}".format(self.y_name), "Children"]
        else:
            return ["Children"]
    elif object_name == self.y_name.value:
        result = ["Parent"]

        if self.find_parent_child_distances != D_NONE:
            result += [C_DISTANCE]

        return result

    return []
# Buggy code
def __init__(self):
    super(AboutDialogInfo, self).__init__()

    self.Copyright = (
        "Copyright © 2003 - 2016 Broad Institute, Inc.\nAll rights reserved."
    )

    self.Name = "CellProfiler"

    self.Version = pkg_resources.get_distribution("cellprofiler").version


# Traceback (UnicodeDecodeError)
Traceback (most recent call last):
File "/Applications/CellProfiler_nightly_20160406.app/Contents/Resources/lib/python2.7/cellprofiler/gui/cpframe.py", line 981, in about
File "/Applications/CellProfiler_nightly_20160406.app/Contents/Resources/lib/python2.7/cellprofiler/gui/dialog.py", line 11, in __init__
File "wx/_misc.pyc", line 6672, in SetCopyright
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc2 in position 10: ordinal not in range(128)

# Fixed code
def __init__(self):
    super(AboutDialogInfo, self).__init__()

    self.Copyright = (
        "Copyright © 2003 - 2016 Broad Institute, Inc.\nAll rights reserved."
    )

    self.Name = "CellProfiler"

    self.Version = "Nightly"
# Buggy code
def save_preferences(self, event):
    event.Skip()
    p = self.get_preferences()
    for control, (text, getter, setter, ui_info, help_text) in zip(self.controls, p):
        if ui_info == COLOR:
            setter(control.BackgroundColour)
        elif ui_info == FILEBROWSE and os.path.isfile(control.Value):
            setter(control.Value)
        else:
            setter(control.Value)


# Traceback (OSError)
Traceback (most recent call last):
File "/Users/dlogan/github/CellProfiler/cellprofiler/gui/cpfigure.py", line 1901, in show_image
image = load_image_url(url)
File "/Users/dlogan/github/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/bioformats/formatreader.py", line 523, in load_using_bioformats_url
with ImageReader(url=url) as rdr:
File "/Users/dlogan/github/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/bioformats/formatreader.py", line 621, in __init__
class_list = get_class_list()
File "/Users/dlogan/github/CellProfiler/cellprofiler/utilities/cpjvm.py", line 202, in get_class_list
dir=cpprefs.get_temporary_directory())
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tempfile.py", line 308, in mkstemp
return _mkstemp_inner(dir, prefix, suffix, flags)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tempfile.py", line 239, in _mkstemp_inner
fd = _os.open(file, flags, 0600)
OSError: [Errno 2] No such file or directory: '/var/folders/8s/r38hcm0s0f3b9cms92c7xlsr0000gp/T/tmpnXIcpJ.garbage'

# Fixed code
def save_preferences(self, event):
    event.Skip()
    p = self.get_preferences()
    for control, (text, getter, setter, ui_info, help_text) in zip(self.controls, p):
        if ui_info == COLOR:
            value = control.BackgroundColour
        elif ui_info == FILEBROWSE:
            value = control.Value
            if not os.path.isfile(value):
                continue
        elif ui_info == DIRBROWSE:
            value = control.Value
            if not os.path.isdir(value):
                continue
        else:
            value = control.Value
        if value != getter():
            setter(value)
# Buggy code
def __ensure_cache_file(self):
    if self.__image_cache_file is None:
        h, self.__image_cache_path = tempfile.mkstemp(
            suffix=".h5", prefix="CellProfilerImageCache"
        )
        self.__image_cache_file = h5py.File(self.__image_cache_path, "w")
        self.__hdf5_object_set = HDF5ObjectSet(self.__image_cache_file)
        os.close(h)


# Traceback (RuntimeError)
Thu Jul 23 15:34:18 2015: Image # 1154, module NamesAndTypes # 3: 0.37 sec
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
File "/home/pmt3sw/CellProfiler/CellProfiler.py", line 279, in main
run_pipeline_headless(options, args)
File "/home/pmt3sw/CellProfiler/CellProfiler.py", line 982, in run_pipeline_headless
measurements.close()
File "/nv/blue/pmt3sw/CellProfiler/cellprofiler/measurements.py", line 359, in close
self.__image_cache_file.flush()
File "/share/apps/anaconda/2.2/lib/python2.7/site-packages/h5py/_hl/files.py", line 263, in flush
h5f.flush(self.fid)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (-------src-dir-------/h5py-2.4.0/h5py/_objects.c:2405)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (-------src-dir-------/h5py-2.4.0/h5py/_objects.c:2362)
File "h5py/h5f.pyx", line 109, in h5py.h5f.flush (-------src-dir-------/h5py-2.4.0/h5py/h5f.c:2044)
RuntimeError: Unable to flush file's cached information (File write failed: time = thu jul 23 15:34:19 2015
, filename = '/tmp/cellprofilerimagecachefb4pgg.h5', file descriptor = 231, errno = 28, error message = 'no space left on device', buf = 0x4b68198, total write size = 4096, bytes this sub-write = 4096, bytes actually written = 18446744073709551615, offset = 32097336)
Failed to stop Ilastik

# Fixed code
def __ensure_cache_file(self):
    if self.__image_cache_file is None:
        path = cpprefs.get_temporary_directory()
        if (
            (path is None)
            or (not os.path.exists(path))
            or (not os.access(path, os.W_OK))
        ):
            path = None
        h, self.__image_cache_path = tempfile.mkstemp(
            dir=path, suffix=".h5", prefix="CellProfilerImageCache"
        )
        self.__image_cache_file = h5py.File(self.__image_cache_path, "w")
        self.__hdf5_object_set = HDF5ObjectSet(self.__image_cache_file)
        os.close(h)
# Buggy code
def align(self, workspace, input1_name, input2_name):
    """Align the second image with the first

    Calculate the alignment offset that must be added to indexes in the
    first image to arrive at indexes in the second image.

    Returns the x,y (not i,j) offsets.
    """
    image1 = workspace.image_set.get_image(input1_name, must_be_grayscale=True)
    image1_pixels = image1.pixel_data
    image2 = workspace.image_set.get_image(input2_name, must_be_grayscale=True)
    image2_pixels = image2.pixel_data
    if self.alignment_method == M_CROSS_CORRELATION:
        return self.align_cross_correlation(image1_pixels, image2_pixels)
    else:
        image1_mask = image1.mask
        image2_mask = image2.mask
        return self.align_mutual_information(
            image1_pixels, image2_pixels, image1_mask, image2_mask
        )


# Traceback (ValueError)
Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.pyc", line 2777, in do_step
File "cellprofiler\modules\maskobjects.pyc", line 244, in run
File "cellprofiler\measurements.pyc", line 1608, in get_image
ValueError: Image was not binary

# Fixed code
def align(self, workspace, input1_name, input2_name):
    """Align the second image with the first

    Calculate the alignment offset that must be added to indexes in the
    first image to arrive at indexes in the second image.

    Returns the x,y (not i,j) offsets.
    """
    image1 = workspace.image_set.get_image(input1_name)
    image1_pixels = image1.pixel_data.astype(float)
    image2 = workspace.image_set.get_image(input2_name)
    image2_pixels = image2.pixel_data.astype(float)
    if self.alignment_method == M_CROSS_CORRELATION:
        return self.align_cross_correlation(image1_pixels, image2_pixels)
    else:
        image1_mask = image1.mask
        image2_mask = image2.mask
        return self.align_mutual_information(
            image1_pixels, image2_pixels, image1_mask, image2_mask
        )
# Buggy code
def __update_sub_menu(self, event, sub_menu, data):
    event.Enable(data.mode != MODE_HIDE)
    event.Text = data.name


# Traceback (PyAssertionError)
Traceback (most recent call last):
File "/Users/dlogan/github/CellProfiler/cellprofiler/gui/pipelinecontroller.py", line 3154, in on_debug_view_workspace
show_workspace_viewer(self.__frame, workspace)
File "/Users/dlogan/github/CellProfiler/cellprofiler/gui/viewworkspace.py", line 41, in show_workspace_viewer
__the_workspace_viewer = ViewWorkspace(parent, workspace)
File "/Users/dlogan/github/CellProfiler/cellprofiler/gui/viewworkspace.py", line 383, in __init__
self.set_workspace(workspace)
File "/Users/dlogan/github/CellProfiler/cellprofiler/gui/viewworkspace.py", line 540, in set_workspace
self.update_menu(self.frame.menu_subplots)
File "/Users/dlogan/github/CellProfiler/cellprofiler/gui/viewworkspace.py", line 554, in update_menu
self.image.on_update_menu(event, menu)
File "/Users/dlogan/github/CellProfiler/cellprofiler/gui/cpartists.py", line 782, in on_update_menu
idx, my_id, name, sub_menu)
File "/usr/local/lib/wxPython-unicode-2.8.12.1/lib/python2.7/site-packages/wx-2.8-mac-unicode/wx/_core.py", line 11120, in InsertMenu
return _core_.Menu_InsertMenu(*args, **kwargs)
PyAssertionError: C++ assertion "wxAssertFailure" failed at /BUILD/wxPython-src-2.8.12.1/src/common/stockitem.cpp(166) in wxGetStockLabel(): invalid stock item ID

# Fixed code
def __update_sub_menu(self, event, sub_menu, data):
    event.Enable(data.mode != MODE_HIDE)
    event.Text = data.name if len(data.name) > 0 else " "
# Buggy code
def validate_module(self, pipeline):
    """Make sure that the module's settings are consistent

    We need at least one image name to be filled in
    """
    if self.scheme_choice != SCHEME_STACK:
        if all(
            [
                color_scheme_setting.image_name.is_blank
                for color_scheme_setting in self.color_scheme_settings
            ]
        ):
            raise cps.ValidationError(
                "At least one of the images must not be blank",
                self.color_scheme_settings[0].image_name.value,
            )


# Traceback (AttributeError)
Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.pyc", line 2777, in do_step
File "cellprofiler\modules\overlayoutlines.pyc", line 208, in run
File "cellprofiler\modules\overlayoutlines.pyc", line 332, in run_color
AttributeError: 'NoneType' object has no attribute 'ndim'

# Fixed code
def validate_module(self, pipeline):
    """Make sure that the module's settings are consistent

    We need at least one image name to be filled in
    """
    if self.scheme_choice != SCHEME_STACK:
        if all(
            [
                color_scheme_setting.image_name.is_blank
                for color_scheme_setting in self.color_scheme_settings
            ]
        ):
            raise cps.ValidationError(
                "At least one of the images must not be blank",
                self.color_scheme_settings[0].image_name,
            )
# Buggy code
def display(self, workspace, figure):
    pm_dict = workspace.display_data.pm_dict
    figure.set_subplots((1, 1))
    if self.title.value != "":
        title = "%s (cycle %s)" % (
            self.title.value,
            workspace.measurements.image_set_number,
        )
    else:
        title = "%s(%s)" % (self.agg_method, self.plot_measurement.value)
    figure.subplot_platemap(0, 0, pm_dict, self.plate_type, title=title)


# Traceback (AttributeError)
Traceback (most recent call last):
File "c:\Trunk\CellProfiler\cellprofiler\gui\pipelinecontroller.py", line 2777, in do_step
module.display(workspace, fig)
File "c:\Trunk\CellProfiler\cellprofiler\modules\displayplatemap.py", line 231, in display
title=title)
File "c:\Trunk\CellProfiler\cellprofiler\gui\cpfigure.py", line 1745, in subplot_platemap
self.Sizer.Insert(0, sz, 0, wx.EXPAND)
AttributeError: 'NoneType' object has no attribute 'Insert'

# Fixed code
def display(self, workspace, figure):
    pm_dict = workspace.display_data.pm_dict
    if not hasattr(figure, "subplots"):
        figure.set_subplots((1, 1))
    if self.title.value != "":
        title = "%s (cycle %s)" % (
            self.title.value,
            workspace.measurements.image_set_number,
        )
    else:
        title = "%s(%s)" % (self.agg_method, self.plot_measurement.value)
    figure.subplot_platemap(0, 0, pm_dict, self.plate_type, title=title)
# Buggy code
def prepare_group(self, workspace, grouping, image_numbers):
    d = self.get_dictionary(workspace.image_set_list)
    d["FIRST_IMAGE"] = True
    if self.save_image_or_figure == IF_MOVIE:
        d["N_FRAMES"] = len(image_numbers)
        d["CURRENT_FRAME"] = 0
    return True


# Traceback (UnboundLocalError)
Traceback (most recent call last):
File "cellprofiler\pipeline.pyc", line 2318, in post_group
File "cellprofiler\modules\saveimages.pyc", line 588, in post_group
File "cellprofiler\modules\saveimages.pyc", line 698, in save_image
UnboundLocalError: local variable 'pixels' referenced before assignment

# Fixed code
def prepare_group(self, workspace, grouping, image_numbers):
    d = self.get_dictionary(workspace.image_set_list)
    if self.save_image_or_figure == IF_MOVIE:
        d["N_FRAMES"] = len(image_numbers)
        d["CURRENT_FRAME"] = 0
    return True
# Buggy code
def run_image(self, workspace):
    """Handle saving an image"""
    #
    # First, check to see if we should save this image
    #
    if self.when_to_save == WS_FIRST_CYCLE:
        d = self.get_dictionary(workspace.image_set_list)
        if not d["FIRST_IMAGE"]:
            workspace.display_data.wrote_image = False
            self.save_filename_measurements(workspace)
            return False
        d["FIRST_IMAGE"] = False

    elif self.when_to_save == WS_LAST_CYCLE:
        workspace.display_data.wrote_image = False
        self.save_filename_measurements(workspace)
        return False
    self.save_image(workspace)
    return True


# Traceback (UnboundLocalError)
Traceback (most recent call last):
File "cellprofiler\pipeline.pyc", line 2318, in post_group
File "cellprofiler\modules\saveimages.pyc", line 588, in post_group
File "cellprofiler\modules\saveimages.pyc", line 698, in save_image
UnboundLocalError: local variable 'pixels' referenced before assignment

# Fixed code
def run_image(self, workspace):
    """Handle saving an image"""
    #
    # First, check to see if we should save this image
    #
    if self.when_to_save == WS_FIRST_CYCLE:
        d = self.get_dictionary(workspace.image_set_list)
        if workspace.measurements[cpmeas.IMAGE, cpmeas.GROUP_INDEX] > 1:
            workspace.display_data.wrote_image = False
            self.save_filename_measurements(workspace)
            return
        d["FIRST_IMAGE"] = False

    elif self.when_to_save == WS_LAST_CYCLE:
        workspace.display_data.wrote_image = False
        self.save_filename_measurements(workspace)
        return
    self.save_image(workspace)
    return True
# Buggy code
def run_objects(self, workspace):
    objects_name = self.objects_name.value
    objects = workspace.object_set.get_objects(objects_name)
    filename = self.get_filename(workspace)
    if filename is None:  # failed overwrite check
        return

    labels = [l for l, c in objects.get_labels()]
    if self.get_file_format() == FF_MAT:
        pixels = objects.segmented
        scipy.io.matlab.mio.savemat(filename, {"Image": pixels}, format="5")

    elif self.gray_or_color == GC_GRAYSCALE:
        if objects.count > 255:
            pixel_type = ome.PT_UINT16
        else:
            pixel_type = ome.PT_UINT8
        for i, l in enumerate(labels):
            self.do_save_image(
                workspace, filename, l, pixel_type, t=i, size_t=len(labels)
            )

    else:
        if self.colormap == cps.DEFAULT:
            colormap = cpp.get_default_colormap()
        else:
            colormap = self.colormap.value
        cm = matplotlib.cm.get_cmap(colormap)

        cpixels = np.zeros((labels[0].shape[0], labels[0].shape[1], 3))
        counts = np.zeros(labels[0].shape, int)
        mapper = matplotlib.cm.ScalarMappable(cmap=cm)
        for pixels in labels:
            cpixels[pixels != 0, :] += mapper.to_rgba(
                distance_color_labels(pixels), bytes=True
            )[pixels != 0, :3]
            counts[pixels != 0] += 1
        counts[counts == 0] = 1
        cpixels = cpixels / counts[:, :, np.newaxis]
        self.do_save_image(workspace, filename, cpixels, ome.PT_UINT8)
    self.save_filename_measurements(workspace)
    if self.show_window:
        workspace.display_data.wrote_image = True


# Traceback (UnboundLocalError)
Traceback (most recent call last):
File "cellprofiler\pipeline.pyc", line 2318, in post_group
File "cellprofiler\modules\saveimages.pyc", line 588, in post_group
File "cellprofiler\modules\saveimages.pyc", line 698, in save_image
UnboundLocalError: local variable 'pixels' referenced before assignment

# Fixed code
def run_objects(self, workspace):
    #
    # First, check to see if we should save this image
    #
    if self.when_to_save == WS_FIRST_CYCLE:
        if workspace.measurements[cpmeas.IMAGE, cpmeas.GROUP_INDEX] > 1:
            workspace.display_data.wrote_image = False
            self.save_filename_measurements(workspace)
            return

    elif self.when_to_save == WS_LAST_CYCLE:
        workspace.display_data.wrote_image = False
        self.save_filename_measurements(workspace)
        return
    self.save_objects(workspace)
# Buggy code
def post_group(self, workspace, *args):
    if self.when_to_save == WS_LAST_CYCLE and self.save_image_or_figure != IF_MOVIE:
        self.save_image(workspace)


# Traceback (UnboundLocalError)
Traceback (most recent call last):
File "cellprofiler\pipeline.pyc", line 2318, in post_group
File "cellprofiler\modules\saveimages.pyc", line 588, in post_group
File "cellprofiler\modules\saveimages.pyc", line 698, in save_image
UnboundLocalError: local variable 'pixels' referenced before assignment

# Fixed code
def post_group(self, workspace, *args):
    if self.when_to_save == WS_LAST_CYCLE and self.save_image_or_figure != IF_MOVIE:
        if self.save_image_or_figure == IF_OBJECTS:
            self.save_objects(workspace)
        else:
            self.save_image(workspace)
# Buggy code
def run_bw(self, workspace):
    image_set = workspace.image_set
    if self.blank_image.value:
        outline_image = image_set.get_image(
            self.outlines[0].outline_name.value, must_be_binary=True
        )
        mask = outline_image.pixel_data
        pixel_data = np.zeros((mask.shape))
        maximum = 1
    else:
        image = image_set.get_image(self.image_name.value, must_be_grayscale=True)
        pixel_data = image.pixel_data
        maximum = 1 if self.max_type == MAX_POSSIBLE else np.max(pixel_data)
        pixel_data = pixel_data.copy()
    for outline in self.outlines:
        mask = self.get_outline(workspace, outline)
        i_max = min(mask.shape[0], pixel_data.shape[0])
        j_max = min(mask.shape[1], pixel_data.shape[1])
        mask = mask[:i_max, :j_max]
        pixel_data[:i_max, :j_max][mask] = maximum
    return pixel_data


# Traceback (ValueError)
Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.pyc", line 2777, in do_step
File "cellprofiler\modules\overlayoutlines.pyc", line 210, in run
File "cellprofiler\modules\overlayoutlines.pyc", line 306, in run_bw
File "cellprofiler\measurements.pyc", line 1578, in get_image
ValueError: The None image is missing from the pipeline.

# Fixed code
def run_bw(self, workspace):
    image_set = workspace.image_set
    if self.blank_image.value:
        shape = self.get_outline(workspace, self.outlines[0]).shape[:2]
        pixel_data = np.zeros(shape)
        maximum = 1
    else:
        image = image_set.get_image(self.image_name.value, must_be_grayscale=True)
        pixel_data = image.pixel_data
        maximum = 1 if self.max_type == MAX_POSSIBLE else np.max(pixel_data)
        pixel_data = pixel_data.copy()
    for outline in self.outlines:
        mask = self.get_outline(workspace, outline)
        i_max = min(mask.shape[0], pixel_data.shape[0])
        j_max = min(mask.shape[1], pixel_data.shape[1])
        mask = mask[:i_max, :j_max]
        pixel_data[:i_max, :j_max][mask] = maximum
    return pixel_data
# Buggy code
def get_mouse_idx(self, event):
    """Return the line index at the event's mouse coordinate"""
    x, y = event.GetPositionTuple()
    line_height = self.line_height + self.leading
    idx = int(y / line_height) + self.GetScrollPos(wx.SB_VERTICAL)
    idx = max(0, min(len(self) - 1, idx))
    if y < line_height:
        # It's the slightly bogus directory at the top
        self.recalc()
        folder_idx = bisect.bisect_right(self.folder_idxs, idx) - 1
        if folder_idx == -1:
            return -1
        idx = self.folder_idxs[folder_idx]
    return idx


# Traceback (IndexError)
Traceback (most recent call last):
File "cellprofiler\gui\pathlist.pyc", line 757, in on_double_click
File "cellprofiler\gui\pathlist.pyc", line 227, in __getitem__
IndexError: index out of bounds

# Fixed code
def get_mouse_idx(self, event):
    """Return the line index at the event's mouse coordinate"""
    if len(self.folder_items) == 0:
        return -1
    x, y = event.GetPositionTuple()
    line_height = self.line_height + self.leading
    idx = int(y / line_height) + self.GetScrollPos(wx.SB_VERTICAL)
    idx = max(0, min(len(self) - 1, idx))
    if y < line_height:
        # It's the slightly bogus directory at the top
        self.recalc()
        folder_idx = bisect.bisect_right(self.folder_idxs, idx) - 1
        if folder_idx == -1:
            return -1
        idx = self.folder_idxs[folder_idx]
    return idx