# encoding: utf-8
"""
Run Fiji is just ImageJ macros headless with python.
"""
import pydebug, subprocess, os, re
from tempfile import mkstemp
import fijibin
# debug with DEBUG=fijibin python script.py
debug = pydebug.debug('fijibin')
##
# Running macros
##
[docs]def run(macro, output_files=[], force_close=True):
"""
Runs Fiji with the suplied macro. Output of Fiji can be viewed by
setting environment variable `DEBUG=fijibin`.
Parameters
----------
macro : string or list of strings
IJM-macro(s) to run. If list of strings, it will be joined with
a space, so all statements should end with ``;``.
output_files : list
Files to check if exists after macro has been run. Files specified that
do not exist after macro is done will print a warning message.
force_close : bool
Will add ``eval("script", "System.exit(42);");`` to end of macro. Exit
code 42 is used to overcome that errors in macro efficiently will exit
Fiji with error code 0. In other words, if this line in the macro is
reached, the macro has most probably finished without errors. This
is the default behaviour.
One should also note that Fiji doesn't terminate right away if
``System.exit()`` is left out, and it may take several minutes for
Fiji to close.
Returns
-------
int
Files from output_files which exists after running macro.
"""
if type(macro) == list:
macro = ' '.join(macro)
if len(macro) == 0:
print('fijibin.macro.run got empty macro, not starting fiji')
return _exists(output_files)
if force_close:
# make sure fiji halts immediately when done
# hack: use error code 42 to check if macro has run sucessfully
macro = macro + 'eval("script", "System.exit(42);");'
# escape backslashes (windows file names)
# not \ \ not \ g1 \\ g2
macro = re.sub(r"([^\\])\\([^\\])", r"\1\\\\\2", macro)
debug('macro {}'.format(macro))
# avoid verbose output of Fiji when DEBUG environment variable set
env = os.environ.copy()
debugging = False
if 'DEBUG' in env:
if env['DEBUG'] == 'fijibin' or env['DEBUG'] == '*':
debugging = True
del env['DEBUG']
fptr, temp_filename = mkstemp(suffix='.ijm')
m = os.fdopen(fptr, 'w')
m.write(macro)
m.flush() # make sure macro is written before running Fiji
m.close()
cmd = [fijibin.BIN, '--headless', '-macro', temp_filename]
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, env=env)
out, err = proc.communicate()
for line in out.decode('latin1', errors='ignore').splitlines():
debug('stdout:' + line)
for line in err.decode('latin1', errors='ignore').splitlines():
debug('stderr:' + line)
if force_close and proc.returncode != 42:
print('fijibin ERROR: Fiji did not successfully ' +
'run macro {}'.format(temp_filename))
if not debugging:
print('fijibin Try running script with ' +
'`DEBUG=fijibin python your_script.py`')
else:
# only delete if everything is ok
os.remove(temp_filename)
# return output_files which exists
return _exists(output_files)
##
# Collection of macros
##
[docs]def stitch(folder, filenames, x_size, y_size, output_filename,
x_start=0, y_start=0, overlap=10):
"""
Creates a Fiji Grid/Collection stitching macro. Parameters are the same as
in the plugin and are described in further detail here:
http://fiji.sc/Image_Stitching#Grid.2FCollection_Stitching.
**Default stitch parameters:**
* Filename defined positions
* Compute overlap
* Subpixel accurancy
* Save computation time (but use more RAM)
* Fusion method: Linear blending
* Regression threshold: 0.30
* Max/avg displacement threshold: 2.50
* Absolute displacement threshold: 3.50
Parameters
----------
folder : string
Path to folder with images or folders with images.
Example: */path/to/slide--S00/chamber--U01--V02/*
filenames : string
Filenames of images.
Example: *field-X{xx}-Y{yy}/image-X{xx}-Y{yy}.ome.tif*
x_size : int
Size of grid, number of images in x direction.
y_size : int
Size of grid, number of images in y direction.
output_filename : string
Where to store fused image. Should be `.png`.
x_start : int
Which x position grid start with.
y_start : int
Which y position grid start with.
overlap : number
Tile overlap in percent. Fiji will find the optimal overlap, but a
precise overlap assumption will decrase computation time.
Returns
-------
string
IJM-macro.
"""
macro = []
macro.append('run("Grid/Collection stitching",')
macro.append('"type=[Filename defined position]')
macro.append('order=[Defined by filename ]')
macro.append('grid_size_x={}'.format(x_size))
macro.append('grid_size_y={}'.format(y_size))
macro.append('tile_overlap={}'.format(overlap))
macro.append('first_file_index_x={}'.format(x_start))
macro.append('first_file_index_y={}'.format(y_start))
macro.append('directory=[{}]'.format(folder))
macro.append('file_names=[{}]'.format(filenames))
macro.append('output_textfile_name=TileConfiguration.txt')
macro.append('fusion_method=[Linear Blending]')
macro.append('regression_threshold=0.20')
macro.append('max/avg_displacement_threshold=2.50')
macro.append('absolute_displacement_threshold=3.50')
macro.append('compute_overlap')
macro.append('subpixel_accuracy')
macro.append('computation_parameters=[Save computation time (but use more RAM)]')
# use display, such that we can specify output filename
# this is 'Fused and display' for previous stitching version!!
macro.append('image_output=[Fuse and display]");')
# save to png
macro.append('selectWindow("Fused");')
macro.append('saveAs("PNG", "{}");'.format(output_filename))
macro.append('close();')
return ' '.join(macro)
##
# Helper functions
##
def _exists(filenames):
"""Check if every filename exists. If not, print an error
message and remove the item from the list.
Parameters
----------
filenames : list
List of filenames to check for existence.
Returns
-------
list
Filtered list of filenames that exists.
"""
exists = []
for filename in filenames:
if os.path.isfile(filename):
exists.append(filename)
else:
print('fijibin ERROR missing output file {}'.format(filename))
return exists