Mercurial > repos > perssond > ashlar

annotate pyramid_upgrade.py @ 1:f183d9de4622 draft

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planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
author goeckslab
date Wed, 24 Aug 2022 19:19:40 +0000
parents b3054f3d42b2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 import argparse
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
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2 import dataclasses
0
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3 import fractions
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4 import io
1
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goeckslab
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5 import os
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6 import re
0
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7 import reprlib
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8 import struct
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9 import sys
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10 import xml.etree.ElementTree
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11 from typing import Any, List
0
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12
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13
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14 datatype_formats = {
1
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15 1: "B", # BYTE
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16 2: "s", # ASCII
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17 3: "H", # SHORT
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18 4: "I", # LONG
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19 5: "I", # RATIONAL (pairs)
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20 6: "b", # SBYTE
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21 7: "B", # UNDEFINED
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22 8: "h", # SSHORT
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23 9: "i", # SLONG
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24 10: "i", # SRATIONAL (pairs)
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25 11: "f", # FLOAT
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26 12: "d", # DOUBLE
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27 13: "I", # IFD
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28 16: "Q", # LONG8
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29 17: "q", # SLONG8
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30 18: "Q", # IFD8
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31 }
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32 rational_datatypes = {5, 10}
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33
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34
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35 class TiffSurgeon:
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36 """Read, manipulate and write IFDs in BigTIFF files."""
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37
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38 def __init__(self, path, *, writeable=False, encoding=None):
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39 self.path = path
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40 self.writeable = writeable
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41 self.encoding = encoding
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42 self.endian = ""
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43 self.ifds = None
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44 self.file = open(self.path, "r+b" if self.writeable else "rb")
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45 self._validate()
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46
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47 def _validate(self):
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48 signature = self.read("2s")
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49 signature = signature.decode("ascii", errors="ignore")
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50 if signature == "II":
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51 self.endian = "<"
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52 elif signature == "MM":
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53 self.endian = ">"
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54 else:
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55 raise FormatError(f"Not a TIFF file (signature is '{signature}').")
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56 version = self.read("H")
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57 if version == 42:
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58 raise FormatError("Cannot process classic TIFF, only BigTIFF.")
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59 offset_size, reserved, first_ifd_offset = self.read("H H Q")
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60 if version != 43 or offset_size != 8 or reserved != 0:
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61 raise FormatError("Malformed TIFF, giving up!")
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62 self.first_ifd_offset = first_ifd_offset
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63
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64 def read(self, fmt, *, file=None):
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65 if file is None:
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66 file = self.file
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67 endian = self.endian or "="
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68 size = struct.calcsize(endian + fmt)
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69 raw = file.read(size)
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70 value = self.unpack(fmt, raw)
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71 return value
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72
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73 def write(self, fmt, *values):
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74 if not self.writeable:
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75 raise ValueError("File is opened as read-only.")
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76 raw = self.pack(fmt, *values)
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77 self.file.write(raw)
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78
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79 def unpack(self, fmt, raw):
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80 assert self.endian or re.match(r"\d+s", fmt), \
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81 "can't unpack non-string before endianness is detected"
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82 fmt = self.endian + fmt
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83 size = struct.calcsize(fmt)
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84 values = struct.unpack(fmt, raw[:size])
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85 if len(values) == 1:
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86 return values[0]
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87 else:
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88 return values
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89
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90 def pack(self, fmt, *values):
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91 assert self.endian, "can't pack without endian set"
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92 fmt = self.endian + fmt
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93 raw = struct.pack(fmt, *values)
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94 return raw
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95
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96 def read_ifds(self):
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97 ifds = [self.read_ifd(self.first_ifd_offset)]
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98 while ifds[-1].offset_next:
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99 ifds.append(self.read_ifd(ifds[-1].offset_next))
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100 self.ifds = ifds
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101
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102 def read_ifd(self, offset):
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103 self.file.seek(offset)
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104 num_tags = self.read("Q")
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105 buf = io.BytesIO(self.file.read(num_tags * 20))
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106 offset_next = self.read("Q")
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107 try:
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108 tags = TagSet([self.read_tag(buf) for i in range(num_tags)])
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109 except FormatError as e:
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110 raise FormatError(f"IFD at offset {offset}, {e}") from None
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111 ifd = Ifd(tags, offset, offset_next)
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112 return ifd
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113
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114 def read_tag(self, buf):
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115 tag = Tag(*self.read("H H Q 8s", file=buf))
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116 value, offset_range = self.tag_value(tag)
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117 tag = dataclasses.replace(tag, value=value, offset_range=offset_range)
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118 return tag
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119
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120 def append_ifd_sequence(self, ifds):
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121 """Write list of IFDs as a chained sequence at the end of the file.
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122
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123 Returns a list of new Ifd objects with updated offsets.
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124
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125 """
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126 self.file.seek(0, os.SEEK_END)
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127 new_ifds = []
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128 for ifd in ifds:
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129 offset = self.file.tell()
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130 self.write("Q", len(ifd.tags))
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131 for tag in ifd.tags:
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132 self.write_tag(tag)
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133 offset_next = self.file.tell() + 8 if ifd is not ifds[-1] else 0
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134 self.write("Q", offset_next)
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135 new_ifd = dataclasses.replace(
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136 ifd, offset=offset, offset_next=offset_next
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137 )
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138 new_ifds.append(new_ifd)
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139 return new_ifds
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140
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141 def append_tag_data(self, code, datatype, value):
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142 """Build new tag and write data to the end of the file if necessary.
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143
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144 Returns a Tag object corresponding to the passed parameters. This
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145 function only writes any "overflow" data and not the IFD entry itself,
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146 so the returned Tag must still be written to an IFD.
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147
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148 If the value is small enough to fit in the data field within an IFD, no
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diff changeset
149 data will actually be written to the file and the returned Tag object
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150 will have the value encoded in its data attribute. Otherwise the data
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151 will be appended to the file and the returned Tag's data attribute will
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152 encode the corresponding offset.
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153
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154 """
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155 fmt = datatype_formats[datatype]
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156 # FIXME Should we perform our own check that values match datatype?
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157 # struct.pack will do it but the exception won't be as understandable.
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158 original_value = value
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diff changeset
159 if isinstance(value, str):
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diff changeset
160 if not self.encoding:
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diff changeset
161 raise ValueError(
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162 "ASCII tag values must be bytes if encoding is not set"
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163 )
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164 value = [value.encode(self.encoding) + b"\x00"]
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165 count = len(value[0])
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166 elif isinstance(value, bytes):
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167 value = [value + b"\x00"]
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168 count = len(value[0])
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diff changeset
169 else:
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diff changeset
170 try:
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diff changeset
171 len(value)
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172 except TypeError:
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173 value = [value]
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174 count = len(value)
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175 struct_count = count
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176 if datatype in rational_datatypes:
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177 value = [i for v in value for i in v.as_integer_ratio()]
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178 count //= 2
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179 byte_count = struct_count * struct.calcsize(fmt)
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180 if byte_count <= 8:
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181 data = self.pack(str(struct_count) + fmt, *value)
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182 data += bytes(8 - byte_count)
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183 else:
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184 self.file.seek(0, os.SEEK_END)
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185 data = self.pack("Q", self.file.tell())
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186 self.write(str(count) + fmt, *value)
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187 # TODO Compute and set offset_range.
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188 tag = Tag(code, datatype, count, data, original_value)
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189 return tag
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190
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191 def write_first_ifd_offset(self, offset):
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192 self.file.seek(8)
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193 self.write("Q", offset)
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194
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195 def write_tag(self, tag):
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196 self.write("H H Q 8s", tag.code, tag.datatype, tag.count, tag.data)
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197
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198 def tag_value(self, tag):
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199 """Return decoded tag data and the file offset range."""
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200 fmt = datatype_formats[tag.datatype]
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201 count = tag.count
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202 if tag.datatype in rational_datatypes:
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203 count *= 2
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204 byte_count = count * struct.calcsize(fmt)
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205 if byte_count <= 8:
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206 value = self.unpack(str(count) + fmt, tag.data)
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207 offset_range = range(0, 0)
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208 else:
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209 offset = self.unpack("Q", tag.data)
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210 self.file.seek(offset)
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211 value = self.read(str(count) + fmt)
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212 offset_range = range(offset, offset + byte_count)
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213 if tag.datatype == 2:
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214 value = value.rstrip(b"\x00")
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215 if self.encoding:
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216 try:
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217 value = value.decode(self.encoding)
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218 except UnicodeDecodeError as e:
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219 raise FormatError(f"tag {tag.code}: {e}") from None
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220 elif tag.datatype in rational_datatypes:
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221 value = [
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222 fractions.Fraction(*v) for v in zip(value[::2], value[1::2])
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223 ]
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224 if len(value) == 1:
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225 value = value[0]
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226 return value, offset_range
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227
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228 def close(self):
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229 self.file.close()
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230
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231
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232 @dataclasses.dataclass(frozen=True)
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233 class Tag:
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234 code: int
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235 datatype: int
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236 count: int
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237 data: bytes
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238 value: Any = None
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239 offset_range: range = None
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240
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241 _vrepr = reprlib.Repr()
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242 _vrepr.maxstring = 60
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243 _vrepr.maxother = 60
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244 vrepr = _vrepr.repr
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245
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246 def __repr__(self):
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247 return (
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248 self.__class__.__qualname__ + "("
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249 + f"code={self.code!r}, datatype={self.datatype!r}, "
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250 + f"count={self.count!r}, data={self.data!r}, "
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251 + f"value={self.vrepr(self.value)}"
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252 + ")"
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253 )
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254
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
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255
0
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256 @dataclasses.dataclass(frozen=True)
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257 class TagSet:
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258 """Container for Tag objects as stored in a TIFF IFD.
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259
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260 Tag objects are maintained in a list that's always sorted in ascending order
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261 by the tag code. Only one tag for a given code may be present, which is where
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262 the "set" name comes from.
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263
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264 """
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265
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266 tags: List[Tag] = dataclasses.field(default_factory=list)
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267
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268 def __post_init__(self):
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269 if len(self.codes) != len(set(self.codes)):
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270 raise ValueError("Duplicate tag codes are not allowed.")
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271
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272 def __repr__(self):
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273 ret = type(self).__name__ + "(["
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274 if self.tags:
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diff changeset
275 ret += "\n"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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parents:
diff changeset
276 ret += "".join([f" {t},\n" for t in self.tags])
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
277 ret += "])"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
278 return ret
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
279
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
280 @property
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
281 def codes(self):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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diff changeset
282 return [t.code for t in self.tags]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
283
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
284 def __getitem__(self, code):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
285 for t in self.tags:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
286 if code == t.code:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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parents:
diff changeset
287 return t
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perssond
parents:
diff changeset
288 else:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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diff changeset
289 raise KeyError(code)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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parents:
diff changeset
290
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
291 def __delitem__(self, code):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
292 try:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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diff changeset
293 i = self.codes.index(code)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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diff changeset
294 except ValueError:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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diff changeset
295 raise KeyError(code) from None
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
parents: 0
diff changeset
296 self.tags[:] = self.tags[:i] + self.tags[i + 1:]
0
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
297
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
298 def __contains__(self, code):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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diff changeset
299 return code in self.codes
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perssond
parents:
diff changeset
300
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
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diff changeset
301 def __len__(self):
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parents:
diff changeset
302 return len(self.tags)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
303
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
304 def __iter__(self):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
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parents:
diff changeset
305 return iter(self.tags)
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perssond
parents:
diff changeset
306
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
307 def get(self, code, default=None):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
308 try:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
309 return self[code]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
310 except KeyError:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
311 return default
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
312
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
313 def get_value(self, code, default=None):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
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diff changeset
314 tag = self.get(code)
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perssond
parents:
diff changeset
315 if tag:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
316 return tag.value
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
317 else:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
318 return default
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
319
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
320 def insert(self, tag):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
321 """Add a new tag or replace an existing one."""
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
322 for i, t in enumerate(self.tags):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
323 if tag.code == t.code:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
324 self.tags[i] = tag
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
325 return
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
326 elif tag.code < t.code:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
327 break
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
328 else:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
329 i = len(self.tags)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
330 n = len(self.tags)
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
parents: 0
diff changeset
331 self.tags[i:n + 1] = [tag] + self.tags[i:n]
0
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
332
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
333
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
334 @dataclasses.dataclass(frozen=True)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
335 class Ifd:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
336 tags: TagSet
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
337 offset: int
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
338 offset_next: int
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
339
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
340 @property
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
341 def nbytes(self):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
342 return len(self.tags) * 20 + 16
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
343
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
344 @property
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
345 def offset_range(self):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
346 return range(self.offset, self.offset + self.nbytes)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
347
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
348
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
349 class FormatError(Exception):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
350 pass
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
351
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
352
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
353 def fix_attrib_namespace(elt):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
354 """Prefix un-namespaced XML attributes with the tag's namespace."""
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
355 # This fixes ElementTree's inability to round-trip XML with a default
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
356 # namespace ("cannot use non-qualified names with default_namespace option"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
357 # error). 7-year-old BPO issue here: https://bugs.python.org/issue17088
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
358 # Code inspired by https://gist.github.com/provegard/1381912 .
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
359 if elt.tag[0] == "{":
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
360 uri, _ = elt.tag[1:].rsplit("}", 1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
361 new_attrib = {}
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
362 for name, value in elt.attrib.items():
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
363 if name[0] != "{":
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
364 # For un-namespaced attributes, copy namespace from element.
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
365 name = f"{{{uri}}}{name}"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
366 new_attrib[name] = value
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
367 elt.attrib = new_attrib
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
368 for child in elt:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
369 fix_attrib_namespace(child)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
370
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
371
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
372 def parse_args():
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
373 parser = argparse.ArgumentParser(
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
374 description="Convert an OME-TIFF legacy pyramid to the BioFormats 6"
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
parents: 0
diff changeset
375 " OME-TIFF pyramid format in-place.",
0
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
376 )
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
377 parser.add_argument("image", help="OME-TIFF file to convert")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
378 parser.add_argument(
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
379 "-n",
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
380 dest="channel_names",
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
381 nargs="+",
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
382 default=[],
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
383 metavar="NAME",
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
384 help="Channel names to be inserted into OME metadata. Number of names"
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
parents: 0
diff changeset
385 " must match number of channels in image. Be sure to put quotes"
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
parents: 0
diff changeset
386 " around names containing spaces or other special shell characters."
0
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
387 )
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
388 args = parser.parse_args()
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
389 return args
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
390
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
391
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
392 def main():
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
393
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
394 args = parse_args()
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
395
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
396 image_path = sys.argv[1]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
397 try:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
398 tiff = TiffSurgeon(image_path, encoding="utf-8", writeable=True)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
399 except FormatError as e:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
400 print(f"TIFF format error: {e}")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
401 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
402
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
403 tiff.read_ifds()
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
404
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
405 # ElementTree doesn't parse xml declarations so we'll just run some sanity
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
406 # checks that we do have UTF-8 and give it a decoded string instead of raw
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
407 # bytes. We need to both ensure that the raw tag bytes decode properly and
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
408 # that the declaration encoding is UTF-8 if present.
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
409 try:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
410 omexml = tiff.ifds[0].tags.get_value(270, "")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
411 except FormatError:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
412 print("ImageDescription tag is not a valid UTF-8 string (not an OME-TIFF?)")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
413 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
414 if re.match(r'<\?xml [^>]*encoding="(?!UTF-8)[^"]*"', omexml):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
415 print("OME-XML is encoded with something other than UTF-8.")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
416 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
417
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
418 xml_ns = {"ome": "http://www.openmicroscopy.org/Schemas/OME/2016-06"}
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
419
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
420 if xml_ns["ome"] not in omexml:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
421 print("Not an OME-TIFF.")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
422 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
423 if (
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
424 "Faas" not in tiff.ifds[0].tags.get_value(305, "")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
425 or 330 in tiff.ifds[0].tags
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
426 ):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
427 print("Not a legacy OME-TIFF pyramid.")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
428 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
429
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
430 # All XML manipulation assumes the document is valid OME-XML!
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
431 root = xml.etree.ElementTree.fromstring(omexml)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
432 image = root.find("ome:Image", xml_ns)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
433 pixels = image.find("ome:Pixels", xml_ns)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
434 size_x = int(pixels.get("SizeX"))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
435 size_y = int(pixels.get("SizeY"))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
436 size_c = int(pixels.get("SizeC"))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
437 size_z = int(pixels.get("SizeZ"))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
438 size_t = int(pixels.get("SizeT"))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
439 num_levels = len(root.findall("ome:Image", xml_ns))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
440 page_dims = [(ifd.tags[256].value, ifd.tags[257].value) for ifd in tiff.ifds]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
441
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
442 if len(root) != num_levels:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
443 print("Top-level OME-XML elements other than Image are not supported.")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
444 if size_z != 1 or size_t != 1:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
445 print("Z-stacks and multiple timepoints are not supported.")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
446 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
447 if size_c * num_levels != len(tiff.ifds):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
448 print("TIFF page count does not match OME-XML Image elements.")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
449 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
450 if any(dims != (size_x, size_y) for dims in page_dims[:size_c]):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
451 print(f"TIFF does not begin with SizeC={size_c} full-size pages.")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
452 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
453 for level in range(1, num_levels):
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
parents: 0
diff changeset
454 level_dims = page_dims[level * size_c: (level + 1) * size_c]
0
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
455 if len(set(level_dims)) != 1:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
456 print(
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
457 f"Pyramid level {level + 1} out of {num_levels} has inconsistent"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
458 f" sizes:\n{level_dims}"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
459 )
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
460 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
461 if args.channel_names and len(args.channel_names) != size_c:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
462 print(
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
463 f"Wrong number of channel names -- image has {size_c} channels but"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
464 f" {len(args.channel_names)} names were specified:"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
465 )
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
466 for i, n in enumerate(args.channel_names, 1):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
467 print(f"{i:4}: {n}")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
468 sys.exit(1)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
469
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
470 print("Input image summary")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
471 print("===================")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
472 print(f"Dimensions: {size_x} x {size_y}")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
473 print(f"Number of channels: {size_c}")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
474 print(f"Pyramid sub-resolutions ({num_levels - 1} total):")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
475 for dim_x, dim_y in page_dims[size_c::size_c]:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
476 print(f" {dim_x} x {dim_y}")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
477 software = tiff.ifds[0].tags.get_value(305, "<not set>")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
478 print(f"Software: {software}")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
479 print()
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
480
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
481 print("Updating OME-XML metadata...")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
482 # We already verified there is nothing but Image elements under the root.
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
483 for other_image in root[1:]:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
484 root.remove(other_image)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
485 for tiffdata in pixels.findall("ome:TiffData", xml_ns):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
486 pixels.remove(tiffdata)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
487 new_tiffdata = xml.etree.ElementTree.Element(
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
488 f"{{{xml_ns['ome']}}}TiffData",
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
489 attrib={"IFD": "0", "PlaneCount": str(size_c)},
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
490 )
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
491 # A valid OME-XML Pixels begins with size_c Channels; then comes TiffData.
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
492 pixels.insert(size_c, new_tiffdata)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
493
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
494 if args.channel_names:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
495 print("Renaming channels...")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
496 channels = pixels.findall("ome:Channel", xml_ns)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
497 for channel, name in zip(channels, args.channel_names):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
498 channel.attrib["Name"] = name
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
499
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
500 fix_attrib_namespace(root)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
501 # ElementTree.tostring would have been simpler but it only supports
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
502 # xml_declaration and default_namespace starting with Python 3.8.
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
503 xml_file = io.BytesIO()
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
504 tree = xml.etree.ElementTree.ElementTree(root)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
505 tree.write(
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
506 xml_file,
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
507 encoding="utf-8",
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
508 xml_declaration=True,
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
509 default_namespace=xml_ns["ome"],
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
510 )
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
511 new_omexml = xml_file.getvalue()
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
512
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
513 print("Writing new TIFF headers...")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
514 stale_ranges = [ifd.offset_range for ifd in tiff.ifds]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
515 main_ifds = tiff.ifds[:size_c]
1
f183d9de4622 planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
goeckslab
parents: 0
diff changeset
516 channel_sub_ifds = [tiff.ifds[c + size_c::size_c] for c in range(size_c)]
0
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
517 for i, (main_ifd, sub_ifds) in enumerate(zip(main_ifds, channel_sub_ifds)):
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
518 for ifd in sub_ifds:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
519 if 305 in ifd.tags:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
520 stale_ranges.append(ifd.tags[305].offset_range)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
521 del ifd.tags[305]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
522 ifd.tags.insert(tiff.append_tag_data(254, 3, 1))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
523 if i == 0:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
524 stale_ranges.append(main_ifd.tags[305].offset_range)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
525 stale_ranges.append(main_ifd.tags[270].offset_range)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
526 old_software = main_ifd.tags[305].value.replace("Faas", "F*a*a*s")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
527 new_software = f"pyramid_upgrade.py (was {old_software})"
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
528 main_ifd.tags.insert(tiff.append_tag_data(305, 2, new_software))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
529 main_ifd.tags.insert(tiff.append_tag_data(270, 2, new_omexml))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
530 else:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
531 if 305 in main_ifd.tags:
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
532 stale_ranges.append(main_ifd.tags[305].offset_range)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
533 del main_ifd.tags[305]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
534 sub_ifds[:] = tiff.append_ifd_sequence(sub_ifds)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
535 offsets = [ifd.offset for ifd in sub_ifds]
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
536 main_ifd.tags.insert(tiff.append_tag_data(330, 16, offsets))
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
537 main_ifds = tiff.append_ifd_sequence(main_ifds)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
538 tiff.write_first_ifd_offset(main_ifds[0].offset)
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
539
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
540 print("Clearing old headers and tag values...")
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
541 # We overwrite all the old IFDs and referenced data values with obvious
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
542 # "filler" as a courtesy to anyone who might need to poke around in the TIFF
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
543 # structure down the road. A real TIFF parser wouldn't see the stale data,
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
544 # but a human might just scan for the first thing that looks like a run of
b3054f3d42b2 "planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
perssond
parents:
diff changeset
545 # OME-XML and not realize it's been replaced with something else. The filler
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546 # content is the repeated string "unused " with square brackets at the
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547 # beginning and end of each filled IFD or data value.
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548 filler = b"unused "
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549 f_len = len(filler)
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550 for r in stale_ranges:
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551 tiff.file.seek(r.start)
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552 tiff.file.write(b"[")
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553 f_total = len(r) - 2
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554 for i in range(f_total // f_len):
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555 tiff.file.write(filler)
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556 tiff.file.write(b" " * (f_total % f_len))
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557 tiff.file.write(b"]")
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558
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559 tiff.close()
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560
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561 print()
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562 print("Success!")
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563
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564
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565 if __name__ == "__main__":
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566 main()