Mercurial > repos > bgruening > cp_measure_image_intensity

comparison starting_modules.py @ 6:b64af54c5c09 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:28:54 +0000
parents 8536b1ae0254
children
comparison
equal deleted inserted replaced
5:8536b1ae0254 6:b64af54c5c09
7 7
8 params = json.load(open(input_json_path, "r")) 8 params = json.load(open(input_json_path, "r"))
9 9
10 10
11 def write_images(): 11 def write_images():
12 filter_images = params['images']['filter_images'] 12 filter_images = params["images"]["filter_images"]
13 13
14 _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" 14 _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
15 _str += FOURSPACES + ":\n" 15 _str += FOURSPACES + ":\n"
16 _str += FOURSPACES + "Filter images?:%s\n" % filter_images 16 _str += FOURSPACES + "Filter images?:%s\n" % filter_images
17 _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n" 17 _str += (
18 FOURSPACES
19 + 'Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")\n'
20 )
18 21
19 return _str 22 return _str
20 23
21 24
22 def write_metadata(): 25 def write_metadata():
23 metadata_extraction = params['metadata']['con_metadata_extraction'] 26 metadata_extraction = params["metadata"]["con_metadata_extraction"]
24 extract = metadata_extraction['extract'] 27 extract = metadata_extraction["extract"]
25 28
26 if 'extraction_method' in metadata_extraction: 29 if "extraction_method" in metadata_extraction:
27 method_count = len(metadata_extraction['extraction_method']) 30 method_count = len(metadata_extraction["extraction_method"])
28 else: 31 else:
29 method_count = 1 32 method_count = 1
30 33
31 _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" 34 _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
32 _str += FOURSPACES + "Extract metadata?:%s\n" % extract 35 _str += FOURSPACES + "Extract metadata?:%s\n" % extract
33 36
34 if extract == "No": 37 if extract == "No":
35 _str += FOURSPACES + "Metadata data type:Text\n" 38 _str += FOURSPACES + "Metadata data type:Text\n"
36 _str += FOURSPACES + "Metadata types:{}\n" 39 _str += FOURSPACES + "Metadata types:{}\n"
37 _str += FOURSPACES + "Extraction method count:%d\n" % method_count 40 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
38 _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n" 41 _str += (
39 _str += FOURSPACES + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n" 42 FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
40 _str += FOURSPACES + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n" 43 )
44 _str += (
45 FOURSPACES
46 + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n"
47 )
48 _str += (
49 FOURSPACES
50 + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
51 )
41 _str += FOURSPACES + "Extract metadata from:All images\n" 52 _str += FOURSPACES + "Extract metadata from:All images\n"
42 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" 53 _str += (
54 FOURSPACES + 'Select the filtering criteria:and (file does contain "")\n'
55 )
43 _str += FOURSPACES + "Metadata file location:\n" 56 _str += FOURSPACES + "Metadata file location:\n"
44 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n" 57 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
45 _str += FOURSPACES + "Use case insensitive matching?:No\n" 58 _str += FOURSPACES + "Use case insensitive matching?:No\n"
46 else: 59 else:
47 _str += FOURSPACES + "Metadata data type:Text\n" # default Text,not possible to select in Galaxy 60 _str += (
61 FOURSPACES + "Metadata data type:Text\n"
62 ) # default Text,not possible to select in Galaxy
48 _str += FOURSPACES + "Metadata types:{}\n" 63 _str += FOURSPACES + "Metadata types:{}\n"
49 _str += FOURSPACES + "Extraction method count:%d\n" % method_count 64 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
50 65
51 for methods in metadata_extraction["extraction_method"]: 66 for methods in metadata_extraction["extraction_method"]:
52 _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"] 67 _str += (
53 _str += FOURSPACES + "Metadata source:%s\n" % methods["con_metadata_source"]["metadata_source"] 68 FOURSPACES
69 + "Metadata extraction method:%s\n"
70 % methods["metadata_extraction_method"]
71 )
72 _str += (
73 FOURSPACES
74 + "Metadata source:%s\n"
75 % methods["con_metadata_source"]["metadata_source"]
76 )
54 77
55 if "file_name_regex" in methods["con_metadata_source"]: 78 if "file_name_regex" in methods["con_metadata_source"]:
56 file_regex = methods["con_metadata_source"]["file_name_regex"] 79 file_regex = methods["con_metadata_source"]["file_name_regex"]
57 folder_regex = "(?P<folderField1>.*)" 80 folder_regex = "(?P<folderField1>.*)"
58 elif "folder_name_regex" in methods["con_metadata_source"]: 81 elif "folder_name_regex" in methods["con_metadata_source"]:
61 else: 84 else:
62 # default regex 85 # default regex
63 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)" 86 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
64 folder_regex = "(?P<folderField1>.*)" 87 folder_regex = "(?P<folderField1>.*)"
65 88
66 _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % file_regex 89 _str += (
67 _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % folder_regex 90 FOURSPACES
68 91 + "Regular expression to extract from file name:%s\n" % file_regex
69 _str += FOURSPACES + "Extract metadata from:%s\n" % methods["con_metadata_extract_from"]["extract_metadata_from"] 92 )
70 93 _str += (
71 if methods["con_metadata_extract_from"]["extract_metadata_from"] == "Images matching a rule": 94 FOURSPACES
95 + "Regular expression to extract from folder name:%s\n" % folder_regex
96 )
97
98 _str += (
99 FOURSPACES
100 + "Extract metadata from:%s\n"
101 % methods["con_metadata_extract_from"]["extract_metadata_from"]
102 )
103
104 if (
105 methods["con_metadata_extract_from"]["extract_metadata_from"]
106 == "Images matching a rule"
107 ):
72 rule_str = "" 108 rule_str = ""
73 for r in methods["con_metadata_extract_from"]["r_match"]: 109 for r in methods["con_metadata_extract_from"]["r_match"]:
74 if r["con_match"]["rule_type"] == "extension": 110 if r["con_match"]["rule_type"] == "extension":
75 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \ 111 rule_str += (
76 r["con_match"]["match_type"] + ")" 112 " ("
113 + r["con_match"]["rule_type"]
114 + " "
115 + r["con_match"]["operator"]
116 + " "
117 + r["con_match"]["match_type"]
118 + ")"
119 )
77 else: 120 else:
78 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\ 121 rule_str += (
79 r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")" 122 " ("
80 123 + r["con_match"]["rule_type"]
81 _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str + "\n" 124 + " "
82 else: 125 + r["con_match"]["operator"]
83 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" # this line is required even if it's not used 126 + " "
127 + r["con_match"]["contain"]
128 + ' "'
129 + r["con_match"]["match_value"]
130 + '")'
131 )
132
133 _str += (
134 FOURSPACES
135 + "Select the filtering criteria:"
136 + methods["con_metadata_extract_from"]["match_all_any"]
137 + rule_str
138 + "\n"
139 )
140 else:
141 _str += (
142 FOURSPACES
143 + 'Select the filtering criteria:and (file does contain "")\n'
144 ) # this line is required even if it's not used
84 145
85 _str += FOURSPACES + "Metadata file location:\n" 146 _str += FOURSPACES + "Metadata file location:\n"
86 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n" 147 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
87 _str += FOURSPACES + "Use case insensitive matching?:No\n" 148 _str += FOURSPACES + "Use case insensitive matching?:No\n"
88 149
89 return _str 150 return _str
90 151
91 152
92 def write_nameandtypes(): 153 def write_nameandtypes():
93 nameandtypes = params['nameandtypes'] 154 nameandtypes = params["nameandtypes"]
94 assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to'] 155 assign_a_name = nameandtypes["con_assign_a_name_to"]["assign_a_name_to"]
95 156
96 if "con_select_image_type" in nameandtypes['con_assign_a_name_to']: 157 if "con_select_image_type" in nameandtypes["con_assign_a_name_to"]:
97 con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity'] 158 con_set_intensity = nameandtypes["con_assign_a_name_to"][
98 max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0 159 "con_select_image_type"
160 ]["con_set_intensity"]
161 max_intensity = (
162 con_set_intensity["maximum_intensity"]
163 if "maximum_intensity" in con_set_intensity
164 else 255.0
165 )
99 else: 166 else:
100 max_intensity = 255.0 167 max_intensity = 255.0
101 168
102 pixel_space = nameandtypes['pixel_space'] 169 pixel_space = nameandtypes["pixel_space"]
103 170
104 rule_count = len(nameandtypes['con_assign_a_name_to']['r_match_rule']) if "r_match_rule" in nameandtypes['con_assign_a_name_to'] else 1 171 rule_count = (
105 172 len(nameandtypes["con_assign_a_name_to"]["r_match_rule"])
106 process_3d = nameandtypes['pixel_space']['process_3d'] 173 if "r_match_rule" in nameandtypes["con_assign_a_name_to"]
174 else 1
175 )
176
177 process_3d = nameandtypes["pixel_space"]["process_3d"]
107 x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"] 178 x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
108 y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"] 179 y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
109 z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"] 180 z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
110 181
111 _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" 182 _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
112 183
113 _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name 184 _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
114 185
115 if assign_a_name == "All images": 186 if assign_a_name == "All images":
116 _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type'] 187 _str += (
117 _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign'] 188 FOURSPACES
189 + "Select the image type:%s\n"
190 % nameandtypes["con_assign_a_name_to"]["con_select_image_type"][
191 "select_image_type"
192 ]
193 )
194 _str += (
195 FOURSPACES
196 + "Name to assign these images:%s\n"
197 % nameandtypes["con_assign_a_name_to"]["name_to_assign"]
198 )
118 _str += FOURSPACES + "Match metadata:[]\n" 199 _str += FOURSPACES + "Match metadata:[]\n"
119 200
120 _str += FOURSPACES + "Image set matching method:Order\n" 201 _str += FOURSPACES + "Image set matching method:Order\n"
121 _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from'] 202 _str += (
203 FOURSPACES
204 + "Set intensity range from:%s\n"
205 % con_set_intensity["set_intensity_range_from"]
206 )
122 _str += FOURSPACES + "Assignments count:%s\n" % rule_count 207 _str += FOURSPACES + "Assignments count:%s\n" % rule_count
123 _str += FOURSPACES + "Single images count:0\n" 208 _str += FOURSPACES + "Single images count:0\n"
124 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity 209 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
125 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d 210 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
126 211
128 # the below lines are not relevant to "images matching rules", but needed in pipeline file 213 # the below lines are not relevant to "images matching rules", but needed in pipeline file
129 _str += FOURSPACES + "Select the image type:Grayscale image\n" 214 _str += FOURSPACES + "Select the image type:Grayscale image\n"
130 _str += FOURSPACES + "Name to assign these images:DNA\n" 215 _str += FOURSPACES + "Name to assign these images:DNA\n"
131 _str += FOURSPACES + "Match metadata:[]\n" 216 _str += FOURSPACES + "Match metadata:[]\n"
132 217
133 _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method'] 218 _str += (
219 FOURSPACES
220 + "Image set matching method:%s\n"
221 % nameandtypes["con_assign_a_name_to"]["matching_method"]
222 )
134 _str += FOURSPACES + "Set intensity range from:Image metadata\n" 223 _str += FOURSPACES + "Set intensity range from:Image metadata\n"
135 _str += FOURSPACES + "Assignments count:%d\n" % rule_count 224 _str += FOURSPACES + "Assignments count:%d\n" % rule_count
136 _str += FOURSPACES + "Single images count:0\n" 225 _str += FOURSPACES + "Single images count:0\n"
137 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity 226 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
138 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d 227 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
145 for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]: 234 for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
146 235
147 rule_str = "" 236 rule_str = ""
148 if len(rule["r_match"]) > 0: 237 if len(rule["r_match"]) > 0:
149 for r in rule["r_match"]: 238 for r in rule["r_match"]:
150 if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory": 239 if (
151 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \ 240 r["con_match"]["rule_type"] == "file"
152 r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")" 241 or r["con_match"]["rule_type"] == "directory"
242 ):
243 rule_str += (
244 " ("
245 + r["con_match"]["rule_type"]
246 + " "
247 + r["con_match"]["operator"]
248 + " "
249 + r["con_match"]["contain"]
250 + ' "'
251 + r["con_match"]["match_value"]
252 + '")'
253 )
153 else: 254 else:
154 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \ 255 rule_str += (
155 r["con_match"]["match_type"] + ")" 256 " ("
156 else: 257 + r["con_match"]["rule_type"]
157 rule_str = " (file does contain \"\")" # need to have a value even if it is not used 258 + " "
158 259 + r["con_match"]["operator"]
159 _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str + "\n" 260 + " "
261 + r["con_match"]["match_type"]
262 + ")"
263 )
264 else:
265 rule_str = ' (file does contain "")' # need to have a value even if it is not used
266
267 _str += (
268 FOURSPACES
269 + "Select the rule criteria:"
270 + rule["match_all_any"]
271 + rule_str
272 + "\n"
273 )
160 274
161 img_or_obj = rule["con_select_image_type"]["select_image_type"] 275 img_or_obj = rule["con_select_image_type"]["select_image_type"]
162 276
163 if img_or_obj == "Objects": 277 if img_or_obj == "Objects":
164 _str += FOURSPACES + "Name to assign these images:DNA\n" 278 _str += FOURSPACES + "Name to assign these images:DNA\n"
165 _str += FOURSPACES + "Name to assign these objects:%s\n" % rule["con_select_image_type"]["name_to_assign"] 279 _str += (
166 else: 280 FOURSPACES
167 _str += FOURSPACES + "Name to assign these images:%s\n" % rule["con_select_image_type"]["name_to_assign"] 281 + "Name to assign these objects:%s\n"
282 % rule["con_select_image_type"]["name_to_assign"]
283 )
284 else:
285 _str += (
286 FOURSPACES
287 + "Name to assign these images:%s\n"
288 % rule["con_select_image_type"]["name_to_assign"]
289 )
168 _str += FOURSPACES + "Name to assign these objects:Cell\n" 290 _str += FOURSPACES + "Name to assign these objects:Cell\n"
169 291
170 _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj 292 _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj
171 293
172 intensity_range = "Image metadata" # default value 294 intensity_range = "Image metadata" # default value
173 if img_or_obj == "Grayscale image" or img_or_obj == "Color image": 295 if img_or_obj == "Grayscale image" or img_or_obj == "Color image":
174 intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"] 296 intensity_range = rule["con_select_image_type"]["con_set_intensity"][
297 "set_intensity_range_from"
298 ]
175 299
176 _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range 300 _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
177 301
178 if intensity_range == "Manual": 302 if intensity_range == "Manual":
179 _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"] 303 _str += (
304 FOURSPACES
305 + "Maximum intensity:%s\n"
306 % rule["con_select_image_type"]["con_set_intensity"][
307 "maximum_intensity"
308 ]
309 )
180 else: 310 else:
181 _str += FOURSPACES + "Maximum intensity:255.0\n" 311 _str += FOURSPACES + "Maximum intensity:255.0\n"
182 312
183 return _str 313 return _str
184 314
185 315
186 def write_groups(): 316 def write_groups():
187 groups = params['groups'] 317 groups = params["groups"]
188 318
189 _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" 319 _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
190 320
191 group_images = groups["con_groups"]["group_images"] 321 group_images = groups["con_groups"]["group_images"]
192 322
193 _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images 323 _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images
194 _str += FOURSPACES + "grouping metadata count:1\n" 324 _str += FOURSPACES + "grouping metadata count:1\n"
195 325
196 if group_images == "Yes": 326 if group_images == "Yes":
197 _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"] 327 _str += (
328 FOURSPACES
329 + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
330 )
198 else: 331 else:
199 _str += FOURSPACES + "Metadata category:None\n" 332 _str += FOURSPACES + "Metadata category:None\n"
200 333
201 return _str 334 return _str
202 335
203 336
204 with open("output.cppipe", "w") as f: 337 with open("output.cppipe", "w") as f:
205 headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n", 338 headers = [
206 "Version:3\n", 339 "CellProfiler Pipeline: http://www.cellprofiler.org\n",
207 "DateRevision:319\n", 340 "Version:3\n",
208 "GitHash:\n", 341 "DateRevision:319\n",
209 "ModuleCount:4\n", 342 "GitHash:\n",
210 "HasImagePlaneDetails:False", 343 "ModuleCount:4\n",
211 "\n"] 344 "HasImagePlaneDetails:False",
345 "\n",
346 ]
212 347
213 f.writelines(headers) 348 f.writelines(headers)
214 349
215 img_str = write_images() 350 img_str = write_images()
216 metadata_str = write_metadata() 351 metadata_str = write_metadata()