Added initial IndexedSegment

atrcopy/indexed_segment.py

@@ -0,0 +1,695 @@
+import bisect
+import io
+
+import numpy as np
+
+from . import errors
+from .utils import to_numpy, to_numpy_list, uuid
+from functools import reduce
+
+user_bit_mask = 0x07
+data_style = 0x1
+not_user_bit_mask = 0xff ^ user_bit_mask
+diff_bit_mask = 0x10
+match_bit_mask = 0x20
+comment_bit_mask = 0x40
+selected_bit_mask = 0x80
+
+import logging
+log = logging.getLogger(__name__)
+
+
+def get_style_bits(match=False, comment=False, selected=False, data=False, diff=False, user=0):
+    """ Return an int value that contains the specified style bits set.
+
+    Available styles for each byte are:
+
+    match: part of the currently matched search
+    comment: user commented area
+    selected: selected region
+    data: labeled in the disassembler as a data region (i.e. not disassembled)
+    """
+    style_bits = 0
+    if user:
+        style_bits |= (user & user_bit_mask)
+    if diff:
+        style_bits |= diff_bit_mask
+    if match:
+        style_bits |= match_bit_mask
+    if comment:
+        style_bits |= comment_bit_mask
+    if data:
+        style_bits |= (data_style & user_bit_mask)
+    if selected:
+        style_bits |= selected_bit_mask
+    return style_bits
+
+
+def get_style_mask(**kwargs):
+    """Get the bit mask that, when anded with data, will turn off the
+    selected bits
+    """
+    bits = get_style_bits(**kwargs)
+    if 'user' in kwargs and kwargs['user']:
+        bits |= user_bit_mask
+    else:
+        bits &= (0xff ^ user_bit_mask)
+    return 0xff ^ bits
+
+
+class SourceSegment:
+    can_resize_default = False
+
+    base_serializable_attributes = ['origin', 'error', 'name', 'verbose_name', 'uuid', 'can_resize']
+    extra_serializable_attributes = []
+
+    def __init__(self, data, style=None, origin=0, name="All", error=None, verbose_name=None, memory_map=None):
+        self.origin = int(origin)  # force python int to decouple from possibly being a numpy datatype
+        self.error = error
+        self.name = name
+        self.verbose_name = verbose_name
+        self.uuid = uuid()
+        if memory_map is None:
+            memory_map = {}
+        self.memory_map = memory_map
+        self.comments = dict()
+        self.user_data = dict()
+        for i in range(1, user_bit_mask):
+            self.user_data[i] = dict()
+
+        # Some segments may be resized to contain additional segments not
+        # present when the segment was created.
+        self.can_resize = self.__class__.can_resize_default
+
+        self.set_data(data, style)
+
+    def set_data(self, data, style):
+        self._data = to_numpy(data)
+        if style is None:
+            style = np.zeros(len(self._data), dtype=np.uint8)
+        self._style = to_numpy(style)
+
+    @property
+    def data(self):
+        return self._data
+
+    @property
+    def style(self):
+        return self._style
+
+    def __len__(self):
+        return np.alen(self._data)
+
+    def __and__(self, other):
+        return self._data & other
+
+    def __iand__(self, other):
+        self._data &= other
+        return self
+
+    def __getitem__(self, index):
+        return self._data[index]
+
+    def __setitem__(self, index, value):
+        self._data[index] = value
+
+    #### serialization
+
+    def __getstate__(self):
+        """Custom jsonpickle state save routine
+
+        This routine culls down the list of attributes that should be
+        serialized, and in some cases changes their format slightly so they
+        have a better mapping to json objects. For instance, json can't handle
+        dicts with integer keys, so dicts are turned into lists of lists.
+        Tuples are also turned into lists because tuples don't have a direct
+        representation in json, while lists have a compact representation in
+        json.
+        """
+        state = dict()
+        for key in self.base_serializable_attributes:
+            state[key] = getattr(self, key)
+        for key in self.extra_serializable_attributes:
+            state[key] = getattr(self, key)
+        r = self.rawdata
+        state['memory_map'] = sorted([list(i) for i in self.memory_map.items()])
+        state['comment ranges'] = [list(a) for a in self.get_style_ranges(comment=True)]
+        state['data ranges'] = [list(a) for a in self.get_style_ranges(data=True)]
+        for i in range(1, user_bit_mask):
+            r = [list(a) for a in self.get_style_ranges(user=i)]
+            if r:
+                slot = "user style %d" % i
+                state[slot] = r
+
+        # json serialization doesn't allow int keys, so convert to list of
+        # pairs
+        state['comments'] = self.get_sorted_comments()
+        return state
+
+    def __setstate__(self, state):
+        """Custom jsonpickle state restore routine
+
+        The use of jsonpickle to recreate objects doesn't go through __init__,
+        so there will be missing attributes when restoring old versions of the
+        json. Once a version gets out in the wild and additional attributes are
+        added to a segment, a default value should be applied here.
+        """
+        self.memory_map = dict(state.pop('memory_map', []))
+        self.uuid = state.pop('uuid', uuid())
+        self.can_resize = state.pop('can_resize', self.__class__.can_resize_default)
+        comments = state.pop('comments', {})
+        for k, v in e['comments']:
+            self.comments[k] = v
+        ranges = state.pop('comment ranges')
+        if 'comment ranges' in e:
+            self.set_style_ranges(e['comment ranges'], comment=True)
+        if 'data ranges' in e:
+            self.set_style_ranges(e['data ranges'], user=data_style)
+        if 'display list ranges' in e:
+            # DEPRECATED, but supported on read. Converts display list to
+            # disassembly type 0 for user index 1
+            self.set_style_ranges(e['display list ranges'], data=True, user=1)
+            self.set_user_data(e['display list ranges'], 1, 0)
+        if 'user ranges 1' in e:
+            # DEPRECATED, but supported on read. Converts user extra data 0
+            # (antic dl), 1 (jumpman level), and 2 (jumpman harvest) to user
+            # styles 2, 3, and 4. Data is now user style 1.
+            for r, val in e['user ranges 1']:
+                self.set_style_ranges([r], user=val + 2)
+        for i in range(1, user_bit_mask):
+            slot = "user style %d" % i
+            if slot in e:
+                self.set_style_ranges(e[slot], user=i)
+        self.restore_missing_serializable_defaults()
+        self.__dict__.update(state)
+        self.restore_renamed_serializable_attributes()
+
+    #### style
+
+    def set_style_at_indexes(self, indexes, **kwargs):
+        style_bits = get_style_bits(**kwargs)
+        self._style[indexes] |= style_bits
+
+    def clear_style_at_indexes(self, indexes, **kwargs):
+        style_mask = get_style_mask(**kwargs)
+        self.style[indexes] &= style_mask
+
+    def get_style_at_indexes(self, **kwargs):
+        """Return a list of start, end pairs that match the specified style
+        """
+        style_bits = self.get_style_bits(**kwargs)
+        matches = (self._style & style_bits) == style_bits
+        return self.bool_to_ranges(matches)
+
+    def fixup_comments(self):
+        """Remove any style bytes that are marked as commented but have no
+        comment, and add any style bytes where there's a comment but it isn't
+        marked in the style data.
+
+        This happens on the base data, so only need to do this on one segment
+        that uses this base data.
+        """
+        style_base = self.rawdata.style_base
+        comment_text_indexes = np.asarray(list(self.rawdata.extra.comments.keys()), dtype=np.uint32)
+        comment_mask = self.get_style_mask(comment=True)
+        has_comments = np.where(style_base & comment_bit_mask > 0)[0]
+        both = np.intersect1d(comment_text_indexes, has_comments)
+        log.info("fixup comments: %d correctly marked, %d without style, %d empty text" % (np.alen(both), np.alen(comment_text_indexes) - np.alen(both), np.alen(has_comments) - np.alen(both)))
+        style_base &= comment_mask
+        comment_style = self.get_style_bits(comment=True)
+        style_base[comment_text_indexes] |= comment_style
+
+
+class ArrayWrapper:
+    """Wrapper for numpy data so that manipulations can use normal numpy syntax
+    and still affect the data according to the byte ordering.
+
+    Numpy's fancy indexing can't be used for setting set values, so this
+    intermediate layer is needed that defines the __setitem__ method that
+    explicitly references the byte ordering in the data array.
+    """
+
+    def __init__(self, data, order):
+        self.np_data = data
+        self.order = order
+
+    def __str__(self):
+        return f"ArrayWrapper at {hex(id(self))} count={len(self)} order={self.order}"
+
+    def __len__(self):
+        return np.alen(self.order)
+
+    def __and__(self, other):
+        return self.np_data[self.order] & other
+
+    def __iand__(self, other):
+        self.np_data[self.order] &= other
+        return self
+
+    def __getitem__(self, index):
+        return self.np_data[self.order[index]]
+
+    def __setitem__(self, index, value):
+        self.np_data[self.order[index]] = value
+
+
+
+class IndexedSegment:
+    can_resize_default = False
+
+    base_serializable_attributes = ['origin', 'error', 'name', 'verbose_name', 'uuid', 'can_resize']
+    extra_serializable_attributes = []
+
+    def __init__(self, source_segment, offset_or_offset_list, origin=0, name="All", error=None, verbose_name=None, length=None):
+        self.source_segment = source_segment
+        try:
+            start_offset = int(offset_or_offset_list)
+        except TypeError:
+            self.set_offset_from_list(offset_or_offset_list)
+        else:
+            self.set_offset_from_ints(offset_or_offset_list, length)
+        self.verify_offsets()
+
+        self.origin = int(origin)  # force python int to decouple from possibly being a numpy datatype
+        self.error = error
+        self.name = name
+        self.verbose_name = verbose_name
+        self.uuid = uuid()
+
+        # Some segments may be resized to contain additional segments not
+        # present when the segment was created.
+        self.can_resize = self.__class__.can_resize_default
+
+    #### properties
+
+    @property
+    def data(self):
+        return ArrayWrapper(self.source_segment._data, self.offset_into_source)
+
+    @property
+    def style(self):
+        return ArrayWrapper(self.source_segment._style, self.offset_into_source)
+
+    def __len__(self):
+        return np.alen(self.offset_into_source)
+
+    #### dunder methods and convenience functions to operate on data (not style)
+
+    def __str__(self):
+        if self.origin > 0:
+            origin = " @ %04x" % (self.origin)
+        else:
+            origin = ""
+        s = "%s ($%x bytes%s)" % (self.name, len(self), origin)
+        if self.error:
+            s += " " + self.error
+        return s
+
+    def __and__(self, other):
+        return self.source_segment._data[self.offset_into_source] & other
+
+    def __iand__(self, other):
+        self.source_segment._data[self.offset_into_source] &= other
+        return self
+
+    def __getitem__(self, index):
+        return self.source_segment._data[self.offset_into_source[index]]
+
+    def __setitem__(self, index, value):
+        self.source_segment._data[self.offset_into_source[index]] = value
+
+    #### offsets
+
+    def set_offset_from_list(self, offsets):
+        self.offset_into_source = to_numpy_list(offsets)
+
+    def set_offset_from_ints(self, start, length):
+        if length is None:
+            raise errors.InvalidSegmentLength
+        self.offset_into_source = np.arange(start, start + length, dtype=np.uint32)
+
+    def verify_offsets(self):
+        self.enforce_offset_bounds()
+        self.offset_from_source = self.calc_reverse_offsets()
+
+    def enforce_offset_bounds(self):
+        self.offset_into_source = self.offset_into_source[self.offset_into_source < len(self.source_segment)]
+
+    def calc_reverse_offsets(self):
+        # Initialize array to out of range
+        r = np.zeros(len(self.source_segment), dtype=np.int32) - 1
+        r[self.offset_into_source] = np.arange(len(self), dtype=np.int32)
+        valid = np.where(r >= 0)[0]
+        if len(valid) != len(self):
+            raise errors.InvalidSegmentOrder
+        return r
+
+    #### subset
+
+    def create_subset(self, new_order, *args, **kwargs):
+        new_order_of_source = self.offset_into_source[new_order]
+        segment = IndexedSegment(self.source_segment, new_order_of_source, *args, **kwargs)
+        return segment
+
+    #### serialization
+
+    def __getstate__(self):
+        """Custom jsonpickle state save routine
+
+        This routine culls down the list of attributes that should be
+        serialized, and in some cases changes their format slightly so they
+        have a better mapping to json objects. For instance, json can't handle
+        dicts with integer keys, so dicts are turned into lists of lists.
+        Tuples are also turned into lists because tuples don't have a direct
+        representation in json, while lists have a compact representation in
+        json.
+        """
+        state = dict()
+        for key in self.base_serializable_attributes:
+            state[key] = getattr(self, key)
+        for key in self.extra_serializable_attributes:
+            state[key] = getattr(self, key)
+        r = self.rawdata
+        state['offset_into_source'] = self.calc_serialized_offset_into_source()
+        return state
+
+    def __setstate__(self, state):
+        """Custom jsonpickle state restore routine
+
+        The use of jsonpickle to recreate objects doesn't go through __init__,
+        so there will be missing attributes when restoring old versions of the
+        json. Once a version gets out in the wild and additional attributes are
+        added to a segment, a default value should be applied here.
+        """
+        self.memory_map = dict(state.pop('memory_map', []))
+        self.uuid = state.pop('uuid', uuid())
+        self.can_resize = state.pop('can_resize', self.__class__.can_resize_default)
+        self.restore_missing_serializable_defaults()
+        self.__dict__.update(state)
+        self.restore_renamed_serializable_attributes()
+
+    def restore_missing_serializable_defaults(self):
+        """Hook for the future when extra serializable attributes are added to
+        subclasses so new versions of the code can restore old saved files by
+        providing defaults to any missing attributes.
+        """
+        pass
+
+    def restore_renamed_serializable_attributes(self):
+        """Hook for the future if attributes have been renamed. The old
+        attribute names will have been restored in the __dict__.update in
+        __setstate__, so this routine should move attribute values to their new
+        names.
+        """
+        if hasattr(self, 'start_addr'):
+            self.origin = self.start_addr
+            log.debug(f"moving start_addr to origin: {self.start_addr}")
+            delattr(self, 'start_addr')
+
+
+    @property
+    def verbose_info(self):
+        name = self.verbose_name or self.name
+        if self.rawdata.is_indexed:
+            s = "%s ($%04x bytes) non-contiguous file; file index of first byte: $%04x" % (name, len(self), self.rawdata.order[0])
+        else:
+            s = "%s ($%04x bytes)" % (name, len(self))
+        if self.error:
+            s += "  error='%s'" % self.error
+        return s
+
+    def is_valid_index(self, i):
+        return i >= 0 and i < len(self)
+
+    def tobytes(self):
+        return self.source_segment._data[self.offset_into_source].tobytes()
+
+    def get_style_bits(self, **kwargs):
+        return get_style_bits(**kwargs)
+
+    def get_style_mask(self, **kwargs):
+        return get_style_mask(**kwargs)
+
+    def calc_source_indexes_from_ranges(self, ranges):
+        source_indexes = np.zeros(len(self.source_segment), dtype=np.uint8)
+        offsets = self.offset_into_source
+        for start, end in ranges:
+            if end < start:
+                start, end = end, start
+            source_indexes[offsets[start:end]] = 1
+        affected_source_indexes = np.where(source_indexes > 0)[0]
+        return affected_source_indexes
+
+    def set_style_ranges(self, ranges, **kwargs):
+        indexes = self.calc_source_indexes_from_ranges(ranges)
+        self.source_segment.set_style_at_indexes(indexes, **kwargs)
+
+    def clear_style_ranges(self, ranges, **kwargs):
+        indexes = self.calc_source_indexes_from_ranges(ranges)
+        self.source_segment.clear_style_at_indexes(indexes, **kwargs)
+
+    def clear_style_bits(self, **kwargs):
+        self.source_segment.clear_style_at_indexes(self.offset_into_source, **kwargs)
+
+    def get_style_ranges(self, **kwargs):
+        """Return a list of start, end pairs that match the specified style
+        """
+        style_bits = self.get_style_bits(**kwargs)
+        matches = (self.style & style_bits) == style_bits
+        return self.bool_to_ranges(matches)
+
+    def get_comment_locations(self, **kwargs):
+        style_bits = self.get_style_bits(**kwargs)
+        r = self.rawdata.copy()
+        #print len(r.style)
+        #print len(r.style_base)
+        r.style_base[:] &= style_bits
+        comment_indexes = np.asarray(list(self.rawdata.extra.comments.keys()), dtype=np.uint32)
+        #print comment_indexes
+        r.style_base[comment_indexes] |= comment_bit_mask
+        return r.unindexed_style[:]
+
+    def bool_to_ranges(self, matches):
+        w = np.where(matches == True)[0]
+        # split into groups with consecutive numbers
+        groups = np.split(w, np.where(np.diff(w) != 1)[0] + 1)
+        ranges = []
+        for group in groups:
+            if np.alen(group) > 0:
+                ranges.append((int(group[0]), int(group[-1]) + 1))
+        return ranges
+
+    def find_next(self, index, **kwargs):
+        ranges = self.get_style_ranges(**kwargs)
+        if len(ranges) > 0:
+            index_tuple = (index + 1, 0)
+            match_index = bisect.bisect_right(ranges, index_tuple)
+            if match_index >= len(ranges):
+                match_index = 0
+            return ranges[match_index][0]
+        return None
+
+    def find_previous(self, index, **kwargs):
+        ranges = self.get_style_ranges(**kwargs)
+        if len(ranges) > 0:
+            index_tuple = (index - 1, 0)
+            match_index = bisect.bisect_left(ranges, index_tuple)
+            match_index -= 1
+            if match_index < 0:
+                match_index = len(ranges) - 1
+            return ranges[match_index][0]
+        return None
+
+    def set_user_data(self, ranges, user_index, user_data):
+        for start, end in ranges:
+            # FIXME: this is slow
+            for i in range(start, end):
+                rawindex = self.get_raw_index(i)
+                self.rawdata.extra.user_data[user_index][rawindex] = user_data
+
+    def get_user_data(self, index, user_index):
+        rawindex = self.get_raw_index(index)
+        try:
+            return self.rawdata.extra.user_data[user_index][rawindex]
+        except KeyError:
+            return 0
+
+    def get_sorted_user_data(self, user_index):
+        d = self.rawdata.extra.user_data[user_index]
+        indexes = sorted(d.keys())
+        ranges = []
+        start, end, current = None, None, None
+        for i in indexes:
+            if start is None:
+                start = i
+                current = d[i]
+            else:
+                if d[i] != current or i != end:
+                    ranges.append([[start, end], current])
+                    start = i
+                    current = d[i]
+            end = i + 1
+        if start is not None:
+            ranges.append([[start, end], current])
+        return ranges
+
+    def remove_comments_at_indexes(self, indexes):
+        for where_index in indexes:
+            self.remove_comment(where_index)
+
+    def set_comments_at_indexes(self, ranges, indexes, comments):
+        for where_index, comment in zip(indexes, comments):
+            rawindex = self.get_raw_index(where_index)
+            if comment:
+                log.debug("  restoring comment: rawindex=%d, '%s'" % (rawindex, comment))
+                self.rawdata.extra.comments[rawindex] = comment
+            else:
+                try:
+                    del self.rawdata.extra.comments[rawindex]
+                    log.debug("  no comment in original data, removed comment in current data at rawindex=%d" % rawindex)
+                except KeyError:
+                    log.debug("  no comment in original data or current data at rawindex=%d" % rawindex)
+                    pass
+
+    def get_comments_at_indexes(self, indexes):
+        """Get a list of comments at specified indexes"""
+        s = self.style[indexes]
+        has_comments = np.where(s & comment_bit_mask > 0)[0]
+        comments = []
+        for where_index in has_comments:
+            raw = self.get_raw_index(indexes[where_index])
+            try:
+                comment = self.rawdata.extra.comments[raw]
+            except KeyError:
+                comment = None
+            comments.append(comment)
+        return has_comments, comments
+
+    def get_comment_restore_data(self, ranges):
+        """Get a chunk of data (designed to be opaque) containing comments,
+        styles & locations that can be used to recreate the comments on an undo
+        """
+        restore_data = []
+        for start, end in ranges:
+            log.debug("range: %d-%d" % (start, end))
+            styles = self.style[start:end].copy()
+            items = {}
+            for i in range(start, end):
+                rawindex = self.get_raw_index(i)
+                try:
+                    comment = self.rawdata.extra.comments[rawindex]
+                    log.debug("  index: %d rawindex=%d '%s'" % (i, rawindex, comment))
+                    items[i] = (rawindex, comment)
+                except KeyError:
+                    log.debug("  index: %d rawindex=%d NO COMMENT TO SAVE" % (i, rawindex))
+                    items[i] = (rawindex, None)
+
+            restore_data.append((start, end, styles, items))
+        return restore_data
+
+    def restore_comments(self, restore_data):
+        """Restore comment styles and data
+        """
+        for start, end, styles, items in restore_data:
+            log.debug("range: %d-%d" % (start, end))
+            self.style[start:end] = styles
+            for i in range(start, end):
+                rawindex, comment = items[i]
+                if comment:
+                    log.debug("  restoring comment: rawindex=%d, '%s'" % (rawindex, comment))
+                    self.rawdata.extra.comments[rawindex] = comment
+                else:
+                    # no comment in original data, remove any if exists
+                    try:
+                        del self.rawdata.extra.comments[rawindex]
+                        log.debug("  no comment in original data, removed comment in current data at rawindex=%d" % rawindex)
+                    except KeyError:
+                        log.debug("  no comment in original data or current data at rawindex=%d" % rawindex)
+                        pass
+
+    def get_comments_in_range(self, start, end):
+        """Get a list of comments at specified indexes"""
+        comments = {}
+
+        # Naive way, but maybe it's fast enough: loop over all comments
+        # gathering those within the bounds
+        for rawindex, comment in self.rawdata.extra.comments.items():
+            try:
+                index = self.get_index_from_base_index(rawindex)
+            except IndexError:
+                continue
+            if index >= start and index < end:
+                comments[index] = comment
+        return comments
+
+    def set_comment_at(self, index, text):
+        rawindex = self.get_raw_index(index)
+        self.rawdata.extra.comments[rawindex] = text
+
+    def set_comment(self, ranges, text):
+        self.set_style_ranges(ranges, comment=True)
+        for start, end in ranges:
+            self.set_comment_at(start, text)
+
+    def get_comment(self, index):
+        rawindex = self.get_raw_index(index)
+        return self.rawdata.extra.comments.get(rawindex, "")
+
+    def remove_comment(self, index):
+        rawindex = self.get_raw_index(index)
+        try:
+            del self.rawdata.extra.comments[rawindex]
+        except KeyError:
+            pass
+
+    def get_first_comment(self, ranges):
+        start = reduce(min, [r[0] for r in ranges])
+        rawindex = self.get_raw_index(start)
+        return self.rawdata.extra.comments.get(rawindex, "")
+
+    def clear_comment(self, ranges):
+        self.clear_style_ranges(ranges, comment=True)
+        for start, end in ranges:
+            for i in range(start, end):
+                rawindex = self.get_raw_index(i)
+                if rawindex in self.rawdata.extra.comments:
+                    del self.rawdata.extra.comments[rawindex]
+
+    def get_sorted_comments(self):
+        return sorted([[k, v] for k, v in self.rawdata.extra.comments.items()])
+
+    def iter_comments_in_segment(self):
+        start = self.origin
+        start_index = self.get_raw_index(0)
+        end_index = self.get_raw_index(len(self.rawdata))
+        for k, v in self.rawdata.extra.comments.items():
+            if k >= start_index and k < end_index:
+                yield self.rawdata.get_reverse_index(k), v
+
+    def copy_user_data(self, source, index_offset=0):
+        """Copy comments and other user data from the source segment to this
+        segment.
+
+        The index offset is the offset into self based on the index of source.
+        """
+        for index, comment in source.iter_comments_in_segment():
+            self.set_comment_at(index + index_offset, comment)
+
+    def label(self, index, lower_case=True):
+        if lower_case:
+            return "%04x" % (index + self.origin)
+        else:
+            return "%04X" % (index + self.origin)
+
+    @property
+    def search_copy(self):
+        if self._search_copy is None:
+            self._search_copy = self.data.tobytes()
+        return self._search_copy
+
+    def compare_segment(self, other_segment):
+        self.clear_style_bits(diff=True)
+        diff = self.rawdata.data != other_segment.rawdata.data
+        d = diff * np.uint8(diff_bit_mask)
+        self.style |= (diff * np.uint8(diff_bit_mask))
+        log.debug("compare_segment: # entries %d, # diffs: %d" % (len(diff), len(np.where(diff == True)[0])))

test/test_indexed_segment.py

@@ -0,0 +1,499 @@
+from __future__ import print_function
+from builtins import zip
+from builtins import range
+from builtins import object
+import os
+
+import numpy as np
+import pytest
+
+from atrcopy.indexed_segment import SourceSegment, IndexedSegment
+from atrcopy import get_xex, interleave_segments, user_bit_mask, diff_bit_mask
+from atrcopy import errors
+from functools import reduce
+
+
+def get_indexed(segment, num, scale):
+    indexes = np.arange(num) * scale
+    s = segment.create_subset(indexes)
+    return s, indexes
+
+# class TestSegment1:
+#     def setup(self):
+#         self.segments = []
+#         for i in range(8):
+#             data = np.arange(1024, dtype=np.uint8) * i
+#             r = SegmentData(data)
+#             self.segments.append(DefaultSegment(r, i * 1024))
+
+#     def test_xex(self):
+#         items = [
+#             [(0, 1, 2), 0],
+#             ]
+        
+#         for indexes, stuff in items:
+#             s = [self.segments[i] for i in indexes]
+#             s[1].style[0:500] = diff_bit_mask
+#             s[1].set_comment_at(0, "comment 0")
+#             s[1].set_comment_at(10, "comment 10")
+#             s[1].set_comment_at(100, "comment 100")
+#             print(list(s[1].iter_comments_in_segment()))
+#             with pytest.raises(errors.InvalidBinaryFile):
+#                 seg, subseg = get_xex(s, 0xbeef)
+#             seg, subseg = get_xex(s)
+#             assert tuple(seg.data[0:2]) == (0xff, 0xff)
+#             # 2 bytes for the ffff
+#             # 4 bytes per segment for start, end address
+#             # An extra segment has been inserted for the run address!
+#             size = reduce(lambda a, b:a + len(b), subseg, 0)
+#             assert len(seg) == 2 + size
+#             print(id(s[1]), list(s[1].iter_comments_in_segment()))
+#             print(id(subseg[2]), list(subseg[2].iter_comments_in_segment()))
+#             for i, c in s[1].iter_comments_in_segment():
+#                 assert c == subseg[2].get_comment(i + 4)
+#             assert np.all(s[1].style[:] == subseg[2].style[4:])
+
+#     def test_copy(self):
+#         for s in self.segments:
+#             d = s.rawdata
+#             print("orig:", d.data.shape, d.is_indexed, d.data, id(d.data))
+#             c = d.copy()
+#             print("copy", c.data.shape, c.is_indexed, c.data, id(c.data))
+#             assert c.data.shape == s.data.shape
+#             assert id(c) != id(s)
+#             assert np.all((c.data[:] - s.data[:]) == 0)
+#             c.data[0:100] = 1
+#             print(d.data)
+#             print(c.data)
+#             assert not np.all((c.data[:] - s.data[:]) == 0)
+
+
+class TestIndexed:
+    def setup(self):
+        data = np.arange(4096, dtype=np.uint8)
+        data[1::2] = np.repeat(np.arange(16, dtype=np.uint8), 128)
+        self.source = SourceSegment(data)
+        self.segment = IndexedSegment(self.source, 0, length=len(self.source))
+
+    def test_offsets(self):
+        assert np.array_equal(self.segment.offset_into_source, np.arange(len(self.source)))
+
+    def test_subset(self):
+        # get indexed, will result in every 3th byte
+        s, indexes = get_indexed(self.segment, 256, 3)
+        assert np.array_equal(s.offset_into_source, indexes)
+        for i in range(len(indexes)):
+            index_in_source = i * 3
+            assert np.array_equal(s.offset_into_source[i], index_in_source)
+            s[i] = 33
+            assert s[i] == self.source[index_in_source]
+            self.source[index_in_source] = 3
+            assert s[i] == self.source[index_in_source]
+
+        # get indexed into indexed, will result in every 9th byte
+        s2, indexes2 = get_indexed(s, 64, 3)
+        assert np.array_equal(s2.offset_into_source, indexes2 * 3)
+        for i in range(len(indexes2)):
+            index_in_source = i * 9
+            assert np.array_equal(s2.offset_into_source[i], index_in_source)
+            s2[i] = 99
+            assert s2[i] == self.source[index_in_source]
+            self.source[index_in_source] = 9
+            assert s2[i] == self.source[index_in_source]
+
+    # def test_indexed_sub(self):
+    #     base = self.segment
+    #     assert not base.rawdata.is_indexed
+    #     raw = base.rawdata[512:1536]  # 1024 byte segment
+    #     sub = DefaultSegment(raw, 512)
+        
+    #     assert not sub.rawdata.is_indexed
+    #     for i in range(len(sub)):
+    #         ri = sub.get_raw_index(i)
+    #         assert ri == sub.origin + i
+    #         assert sub[i] == base[ri]
+    #     start, end = sub.byte_bounds_offset()
+    #     assert start == 512
+    #     assert end == 1536
+        
+    #     with pytest.raises(IndexError) as e:
+    #         # attempt to get indexes to 1024 * 3... Index to big => fail!
+    #         s, indexes = get_indexed(sub, 1024, 3)
+        
+    #     # try with elements up to 256 * 3
+    #     s, indexes = get_indexed(sub, 256, 3)
+    #     print(sub.data)
+    #     print(indexes)
+    #     print(s.data[:])
+    #     assert s.rawdata.is_indexed
+    #     for i in range(len(indexes)):
+    #         ri = s.get_raw_index(i)
+    #         print(ri, "base[ri]=%d" % base[ri], i, indexes[i], "s[i]=%d" % s[i])
+    #         assert ri == sub.origin + indexes[i]
+    #         assert s[i] == base[ri]
+    #     start, end = s.byte_bounds_offset()
+    #     assert start == 0
+    #     assert end == len(base)
+        
+    #     # get indexed into indexed, will result in every 9th byte
+    #     s2, indexes2 = get_indexed(s, 64, 3)
+    #     assert s2.rawdata.is_indexed
+    #     for i in range(len(indexes2)):
+    #         assert s2.get_raw_index(i) == sub.origin + indexes2[i] * 3
+    #     start, end = s.byte_bounds_offset()
+    #     assert start == 0
+    #     assert end == len(base)
+
+    # def test_interleave(self):
+    #     base = self.segment
+    #     r1 = base.rawdata[512:1024]  # 512 byte segment
+    #     s1 = DefaultSegment(r1, 512)
+    #     r2 = base.rawdata[1024:1536]  # 512 byte segment
+    #     s2 = DefaultSegment(r2, 1024)
+        
+    #     indexes1 = r1.get_indexes_from_base()
+    #     verify1 = np.arange(512, 1024, dtype=np.uint32)
+    #     assert np.array_equal(indexes1, verify1)
+        
+    #     indexes2 = r2.get_indexes_from_base()
+    #     verify2 = np.arange(1024, 1536, dtype=np.uint32)
+    #     assert np.array_equal(indexes2, verify2)
+        
+    #     s = interleave_segments([s1, s2], 2)
+    #     a = np.empty(len(s1) + len(s2), dtype=np.uint8)
+    #     a[0::4] = s1[0::2]
+    #     a[1::4] = s1[1::2]
+    #     a[2::4] = s2[0::2]
+    #     a[3::4] = s2[1::2]
+    #     print(list(s[:]))
+    #     print(list(a[:]))
+    #     print(s.rawdata.order)
+    #     assert np.array_equal(s[:], a)
+        
+    #     s = interleave_segments([s1, s2], 4)
+    #     a = np.empty(len(s1) + len(s2), dtype=np.uint8)
+    #     a[0::8] = s1[0::4]
+    #     a[1::8] = s1[1::4]
+    #     a[2::8] = s1[2::4]
+    #     a[3::8] = s1[3::4]
+    #     a[4::8] = s2[0::4]
+    #     a[5::8] = s2[1::4]
+    #     a[6::8] = s2[2::4]
+    #     a[7::8] = s2[3::4]
+    #     assert np.array_equal(s[:], a)
+
+    # def test_interleave_not_multiple(self):
+    #     base = self.segment
+    #     r1 = base.rawdata[512:1024]  # 512 byte segment
+    #     s1 = DefaultSegment(r1, 512)
+    #     r2 = base.rawdata[1024:1536]  # 512 byte segment
+    #     s2 = DefaultSegment(r2, 1024)
+        
+    #     indexes1 = r1.get_indexes_from_base()
+    #     verify1 = np.arange(512, 1024, dtype=np.uint32)
+    #     assert np.array_equal(indexes1, verify1)
+        
+    #     indexes2 = r2.get_indexes_from_base()
+    #     verify2 = np.arange(1024, 1536, dtype=np.uint32)
+    #     assert np.array_equal(indexes2, verify2)
+        
+    #     s = interleave_segments([s1, s2], 3)
+
+    #     # when interleave size isn't a multiple of the length, the final array
+    #     # will reduce the size of the input array to force it to be a multiple.
+    #     size = (len(s1) // 3) * 3
+    #     assert len(s) == size * 2
+    #     a = np.empty(len(s), dtype=np.uint8)
+    #     a[0::6] = s1[0:size:3]
+    #     a[1::6] = s1[1:size:3]
+    #     a[2::6] = s1[2:size:3]
+    #     a[3::6] = s2[0:size:3]
+    #     a[4::6] = s2[1:size:3]
+    #     a[5::6] = s2[2:size:3]
+    #     assert np.array_equal(s[:], a)
+
+    # def test_interleave_different_sizes(self):
+    #     base = self.segment
+    #     r1 = base.rawdata[512:768]  # 256 byte segment
+    #     s1 = DefaultSegment(r1, 512)
+    #     r2 = base.rawdata[1024:1536]  # 512 byte segment
+    #     s2 = DefaultSegment(r2, 1024)
+        
+    #     indexes1 = r1.get_indexes_from_base()
+    #     verify1 = np.arange(512, 768, dtype=np.uint32)
+    #     assert np.array_equal(indexes1, verify1)
+        
+    #     indexes2 = r2.get_indexes_from_base()
+    #     verify2 = np.arange(1024, 1536, dtype=np.uint32)
+    #     assert np.array_equal(indexes2, verify2)
+        
+    #     s = interleave_segments([s1, s2], 3)
+
+    #     # when interleave size isn't a multiple of the length, the final array
+    #     # will reduce the size of the input array to force it to be a multiple.
+    #     size = (min(len(s1), len(s2)) // 3) * 3
+    #     assert size == (256 // 3) * 3
+    #     assert len(s) == size * 2
+    #     a = np.empty(len(s), dtype=np.uint8)
+    #     a[0::6] = s1[0:size:3]
+    #     a[1::6] = s1[1:size:3]
+    #     a[2::6] = s1[2:size:3]
+    #     a[3::6] = s2[0:size:3]
+    #     a[4::6] = s2[1:size:3]
+    #     a[5::6] = s2[2:size:3]
+    #     assert np.array_equal(s[:], a)
+
+    # def test_copy(self):
+    #     s, indexes = get_indexed(self.segment, 1024, 3)
+    #     c = s.rawdata.copy()
+    #     print(c.data.shape, c.is_indexed)
+    #     print(id(c.data.np_data), id(s.data.np_data))
+    #     assert c.data.shape == s.data.shape
+    #     assert id(c) != id(s)
+    #     assert np.all((c.data[:] - s.data[:]) == 0)
+    #     c.data[0:100] = 1
+    #     assert not np.all((c.data[:] - s.data[:]) == 0)
+
+
+# class TestComments:
+#     def setup(self):
+#         data = np.ones([4000], dtype=np.uint8)
+#         r = SegmentData(data)
+#         self.segment = DefaultSegment(r, 0)
+#         self.sub_segment = DefaultSegment(r[2:202], 2)
+
+#     def test_locations(self):
+#         s = self.segment
+#         s.set_comment([[4,5]], "test1")
+#         s.set_comment([[40,50]], "test2")
+#         s.set_style_ranges([[2,100]], comment=True)
+#         s.set_style_ranges([[200, 299]], data=True)
+#         for i in range(1,4):
+#             for j in range(1, 4):
+#                 # create some with overlapping regions, some without
+#                 r = [500*j, 500*j + 200*i + 200]
+#                 s.set_style_ranges([r], user=i)
+#                 s.set_user_data([r], i, i*10 + j)
+#         r = [100, 200]
+#         s.set_style_ranges([r], user=4)
+#         s.set_user_data([r], 4, 99)
+#         r = [3100, 3200]
+#         s.set_style_ranges([r], user=4)
+#         s.set_user_data([r], 4, 99)
+
+#         s2 = self.sub_segment
+#         print(len(s2))
+#         copy = s2.get_comment_locations()
+#         print(copy)
+#         # comments at 4 and 40 in the original means 2 and 38 in the copy
+#         orig = s.get_comment_locations()
+#         assert copy[2] == orig[4]
+#         assert copy[28] == orig[38]
+
+#     def test_split_data_at_comment(self):
+#         s = self.segment
+#         s.set_style_ranges([[0,1000]], data=True)
+#         for i in range(0, len(s), 25):
+#             s.set_comment([[i,i+1]], "comment at %d" % i)
+
+#         s2 = self.sub_segment
+#         print(len(s2))
+#         copy = s2.get_comment_locations()
+#         print(copy)
+#         # comments at 4 and 40 in the original means 2 and 38 in the copy
+#         orig = s.get_comment_locations()
+#         print(orig[0:200])
+#         assert copy[2] == orig[4]
+#         assert copy[28] == orig[38]
+
+#         r = s2.get_entire_style_ranges([1], user=True)
+#         print(r)
+#         assert r == [((0, 23), 1), ((23, 48), 1), ((48, 73), 1), ((73, 98), 1), ((98, 123), 1), ((123, 148), 1), ((148, 173), 1), ((173, 198), 1), ((198, 200), 1)]
+
+#     def test_split_data_at_comment2(self):
+#         s = self.segment
+#         start = 0
+#         i = 0
+#         for end in range(40, 1000, 40):
+#             s.set_style_ranges([[start, end]], user=i)
+#             start = end
+#             i = (i + 1) % 8
+#         for i in range(0, len(s), 25):
+#             s.set_comment([[i,i+1]], "comment at %d" % i)
+
+#         s2 = self.sub_segment
+#         print(len(s2))
+#         copy = s2.get_comment_locations()
+#         print(copy)
+#         # comments at 4 and 40 in the original means 2 and 38 in the copy
+#         orig = s.get_comment_locations()
+#         print(orig[0:200])
+#         assert copy[2] == orig[4]
+#         assert copy[28] == orig[38]
+
+#         r = s2.get_entire_style_ranges([1], user=user_bit_mask)
+#         print(r)
+#         assert r == [((0, 38), 0), ((38, 48), 1), ((48, 73), 1), ((73, 78), 1), ((78, 118), 2), ((118, 158), 3), ((158, 198), 4), ((198, 200), 5)]
+
+#     def test_restore_comments(self):
+#         s = self.segment
+#         s.set_style_ranges([[0,1000]], data=True)
+#         for i in range(0, len(s), 5):
+#             s.set_comment([[i,i+1]], "comment at %d" % i)
+
+#         s1 = self.segment
+#         print(len(s1))
+#         indexes = [7,12]
+#         r = s1.get_comment_restore_data([indexes])
+#         print(r)
+#         # force clear comments
+#         s1.rawdata.extra.comments = {}
+#         s1.style[indexes[0]:indexes[1]] = 0
+#         r0 = s1.get_comment_restore_data([indexes])
+#         print(r0)
+#         for start, end, style, items in r0:
+#             print(style)
+#             assert np.all(style == 0)
+#             for rawindex, comment in list(items.values()):
+#                 assert not comment
+#         s1.restore_comments(r)
+#         r1 = s1.get_comment_restore_data([indexes])
+#         print(r1)
+#         for item1, item2 in zip(r, r1):
+#             print(item1)
+#             print(item2)
+#             for a1, a2 in zip(item1, item2):
+#                 print(a1, a2)
+#                 if hasattr(a1, "shape"):
+#                     assert np.all(a1 - a2 == 0)
+#                 else:
+#                     assert a1 == a2
+
+#         s2 = self.sub_segment
+#         print(len(s2))
+#         indexes = [5,10]
+#         r = s2.get_comment_restore_data([indexes])
+#         print(r)
+#         # force clear comments
+#         s2.rawdata.extra.comments = {}
+#         s2.style[indexes[0]:indexes[1]] = 0
+#         r0 = s2.get_comment_restore_data([indexes])
+#         print(r0)
+#         for start, end, style, items in r0:
+#             print(style)
+#             assert np.all(style == 0)
+#             for rawindex, comment in list(items.values()):
+#                 assert not comment
+#         s2.restore_comments(r)
+#         r2 = s2.get_comment_restore_data([indexes])
+#         print(r2)
+#         for item1, item2 in zip(r, r2):
+#             print(item1)
+#             print(item2)
+#             for a1, a2 in zip(item1, item2):
+#                 print(a1, a2)
+#                 if hasattr(a1, "shape"):
+#                     assert np.all(a1 - a2 == 0)
+#                 else:
+#                     assert a1 == a2
+
+#         for item1, item2 in zip(r1, r2):
+#             print(item1)
+#             print(item2)
+#             # indexes won't be the same, but rawindexes and comments will
+#             assert np.all(item1[2] - item2[2] == 0)
+#             assert set(item1[3].values()) == set(item2[3].values())
+
+
+# class TestResize:
+#     def setup(self):
+#         data = np.arange(4096, dtype=np.uint8)
+#         data[1::2] = np.repeat(np.arange(16, dtype=np.uint8), 128)
+#         r = SegmentData(data)
+#         self.container = DefaultSegment(r, 0)
+#         self.container.can_resize = True
+
+#     def test_subset(self):
+#         # check to see data a view of some rawdata will be the same when the
+#         # rawdata is resized.
+#         c = self.container
+#         assert not c.rawdata.is_indexed
+#         offset = 1000
+#         s = DefaultSegment(c.rawdata[offset:offset + offset], 0)
+#         assert not s.rawdata.is_indexed
+
+#         # Check that the small view has the same data as its parent
+#         for i in range(offset):
+#             assert s[i] == c[i + offset]
+
+#         # keep a copy of the old raw data of the subset
+#         oldraw = s.rawdata.copy()
+#         oldid = id(s.rawdata)
+
+#         requested = 8192
+#         oldsize, newsize = c.resize(requested)
+#         assert newsize == requested
+#         s.replace_data(c)  # s should point to the same offset in the resized data
+#         assert id(s.rawdata) == oldid  # segment rawdata object should be same
+#         assert id(oldraw.order) == id(s.rawdata.order)  # order the same
+#         for i in range(offset):  # check values compared to parent
+#             assert s[i] == c[i + offset]
+
+#         # check for changes in parent/view reflected so we see that it's
+#         # pointing to the same array in memory
+#         newbase = c.rawdata
+#         newsub = s.rawdata
+#         print(c.rawdata.data[offset:offset+offset])
+#         print(s.rawdata.data[:])
+#         s.rawdata.data[:] = 111
+#         print(c.rawdata.data[offset:offset+offset])
+#         print(s.rawdata.data[:])
+#         for i in range(offset):
+#             assert s[i] == c[i + offset]
+
+#     def test_indexed(self):
+#         c = self.container
+#         assert not c.rawdata.is_indexed
+#         s, indexes = get_indexed(self.container, 1024, 3)
+#         assert s.rawdata.is_indexed
+#         for i in range(len(indexes)):
+#             assert s.get_raw_index(i) == indexes[i]
+#         requested = 8192
+#         oldraw = s.rawdata.copy()
+#         oldid = id(s.rawdata)
+#         oldsize, newsize = c.resize(requested)
+#         assert newsize == requested
+#         s.replace_data(c)
+#         assert id(s.rawdata) == oldid
+#         assert id(oldraw.order) == id(s.rawdata.order)
+#         for i in range(len(indexes)):
+#             assert s.get_raw_index(i) == indexes[i]
+#         newbase = c.rawdata
+#         newsub = s.rawdata
+#         print(c.rawdata.data)
+#         print(s.rawdata.data[:])
+#         s.rawdata.data[:] = 111
+#         print(c.rawdata.data)
+#         print(s.rawdata.data[:])
+#         for i in range(len(indexes)):
+#             assert c.rawdata.data[indexes[i]] == s.rawdata.data[i]
+
+
+
+if __name__ == "__main__":
+    t = TestIndexed()
+    t.setup()
+    t.test_indexed()
+    # t.test_indexed_sub()
+    # t.test_interleave()
+    # t = TestSegment1()
+    # t.setup()
+    # t.test_xex()
+    # t.test_copy()
+    # t = TestComments()
+    # t.setup()
+    # t.test_split_data_at_comment()
+    # t.test_restore_comments()
+    # t = TestResize()
+    # t.setup()
+    # t.test_subset()