Merge 5c7b005 into 80e095b

.gitignore

@@ -37,7 +37,7 @@ nosetests.xml
 .pydevproject
 
 # Temp files
-
+.vscode/
 *~
 
 # Pipy codes

.travis.yml

@@ -3,6 +3,12 @@ python:
   - "3.6"
 # command to install dependencies
 install:
+  - pip install coveralls pytest-cov==2.6 pytest==3.2.3
   - pip install -e .
 # command to run tests
-script: pytest
+script:
+  - python -m pytest -v --cov bioprinter --cov-report term-missing
+
+after_success:
+  - coveralls
+

LICENCE.txt

@@ -1,9 +1,6 @@
-The MIT License (MIT)
-[OSI Approved License]
+MIT License
 
-The MIT License (MIT)
-
-Copyright (c) Edinburgh Genome Foundry 2015
+Copyright (c) 2015 Edinburgh Genome Foundry
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -12,14 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
-
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

@@ -1,33 +1,45 @@
+.. raw:: html
+
+    <p align="center">
+    <img alt="Bioprinter logo" title="Bioprinter" src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/title.png" width="550">
+    <br /><br />
+    </p>
+
+
 BioPrinter
-===========
+==========
+
 .. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter.svg?branch=master
    :target: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter
    :alt: Travis CI build status (Python 3)
 
-Bioprinter (webpage here_ ) is a Python module to produce living art. It transforms an image into files that a liquid dispenser can use to *print* the image to a plate using pigmented yeast or bacteria.
+.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/bioprinter/badge.svg?branch=master
+   :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/bioprinter?branch=master
+
+
+Bioprinter (webpage here_) is a Python package for producing living art. It transforms an image into files that a liquid dispenser can use to *print* the image to a plate using pigmented yeast or bacteria.
 
 Here are two examples of bio-art:
 
 .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_dolly.jpeg
     :align: center
 
-    Dolly drawn with baker yeast (white), violacein-producing yeast (black), and carotene-producing yeast (orange)
+    Dolly drawn with baker yeast (white), violacein-producing yeast (black), and carotene-producing yeast (orange).
 
 
 .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_england.jpeg
     :align: center
 
-    England flag drawn with 3 different strains of the bacterium *E. coli*.
+    British flag drawn with 3 different strains of the bacterium *E. coli*.
 
 These bio-prints (and many others!) were presented at the University of Edinburgh's SynthSys Open days 2016 (strain selection and acoustic printing by Paulina Kanigowska).
 
-Bioprinter is released on Github_ under the MIT licence (¢ Edinburgh Genome Foundry), everyone is welcome to contribute !
+Bioprinter is released on Github_ under the MIT licence (Copyright 2015 Edinburgh Genome Foundry), everyone is welcome to contribute!
 
-Bioprinter was written at the Edinburgh Genome Foundry by Zulko_ after an original idea and Matlab code by Mike Shen (`Mike's project on Github <https://github.com/mshen5/BioPointillism>`_).
+Bioprinter was written at the Edinburgh Genome Foundry by Zulko_ after an original idea and Matlab code by Mike Shen (`project on Github <https://github.com/mshen5/BioPointillism>`_).
 
 Installation
---------------
-
+------------
 
 If you have PIP installed: ::
 
@@ -39,32 +51,32 @@ Or unzip the source code in a directory and type in a terminal: ::
 
 
 Usage
---------
+-----
 
-In the same folder as your code, place an image. It can have any resolution, but keep in mind that the width/height ratio of the plate it is printed on is 1.5. Make sure that a specific color is used to mark the un-pigmented background of the image, here we use blue:
+The image file to be printed can have any resolution, but note that the width/height ratio of the plate the image is printed on is 1.5. Ensure that a specific color is used to mark the un-pigmented background of the image, here we use blue:
 
 .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/dolly.jpeg
     :align: center
 
-Then write the following code in ``dolly.py``:
+Run the following code in Python or save in ``dolly.py``:
 
 .. code:: python
 
     from bioprinter import bioprint
 
     bioprint(
-        image_filename="../docs/_static/images/dolly.jpeg",
+        image_filename="/path/to/image/dolly.jpeg",
         output_filename="dolly.csv",
-        bg_color=[0, 0, 255], # blue background represents empty wells
-        pigments_wells={"A1": [0, 0, 0],  # black yeast in source well A1
-                        "A2": [250, 120, 10],  # orange yeast in well A2
-                        "A3": [255, 255, 255]},  # white yeast in well A3
+        bg_color=[0, 0, 255],  # blue background represents empty wells
+        pigments_wells={"A1": [0, 0, 0],        # black yeast in source well A1
+                        "A2": [250, 120, 10],   # orange yeast in well A2
+                        "A3": [255, 255, 255]}, # white yeast in well A3
         quantified_image_filename="dolly_preview.jpeg"
     )
 
-Execute in a terminal with ``python dolly.py``. This will produce a ``dolly.csv`` file as well as a preview image of the final printing (so that you can check if the image looks good at this low resolution).
+The saved script can be executed in a terminal with ``python dolly.py``. This will produce a ``dolly.csv`` file as well as a preview image of the final printing (so that you can check if the image looks good at this low resolution).
 
-Prepare a source plate with the right pigmented yeasts in wells A1, A2, A3, use an agar plate as the destination plate, and feed ``dolly.csv`` to the `Labcyte Echo <http://www.labcyte.com/products/liquidhandling/echo-555-liquid-handler>`_. Once the printing is finished, incubate 2 days at 30C (it would be one day at 37C for bacteria). Enjoy the result !
+Prepare a source plate with the right pigmented yeasts in wells A1, A2, A3, use an agar plate as the destination plate, and feed ``dolly.csv`` to the `Labcyte Echo Acoustic Liquid Handler <https://www.labcyte.com/products/liquid-handling/echo-liquid-handlers>`_ (tested with Labcyte Echo 555 Series). Once the printing is finished, incubate 2 days at 30C (it would be one day at 37C for bacteria). Enjoy the result!
 
 
 .. _here: http://edinburgh-genome-foundry.github.io/bioprinter/

bioprinter/__init__.py

@@ -14,4 +14,3 @@
 from .bioprinter import bioprint
 
 from .version import __version__
-

bioprinter/bioprinter.py

@@ -16,6 +16,7 @@
 import numpy as np
 from PIL import Image
 
+
 def _rownumber_to_rowname(num):
     """Return the row name corresponding to the row number.
 
@@ -24,22 +25,30 @@ def _rownumber_to_rowname(num):
     if num < 26:
         return "ABCDEFGHIJKLMNOPQRSTUVWXYZ"[num]
     else:
-        return "".join([_rownumber_to_rowname(int(num / 26) - 1),
-                        _rownumber_to_rowname(num % 26)])
+        return "".join(
+            [_rownumber_to_rowname(int(num / 26) - 1), _rownumber_to_rowname(num % 26)]
+        )
 
 
-def bioprint(image_filename, output_filename, bg_color, pigments_wells,
-             resolution=(192, 128), transfer_volume=2.5,
-             pigment_well_capacity=25000, transfer_rate=150,
-             quantified_image_filename=None):
+def bioprint(
+    image_filename,
+    output_filename,
+    bg_color,
+    pigments_wells,
+    resolution=(192, 128),
+    transfer_volume=2.5,
+    pigment_well_capacity=25000,
+    transfer_rate=150,
+    quantified_image_filename=None,
+):
     """Generate a CSV that can be used in the Echo to print the given picture.
 
     Example
     =======
 
         # Let's print the EGF logo !
         bioprint(
-             img_filename = "egf_logo.jpeg",
+             image_filename = "egf_logo.jpeg",
              output_filename = "egf_logo.csv",
              bg_color=[255,255,255], # The background of the image is white
              pigments_wells= { "A1": [0,0,0],  # black
@@ -82,7 +91,7 @@ def bioprint(image_filename, output_filename, bg_color, pigments_wells,
       value on our Echo.
 
     pigment_well_capacity
-      Volume in microliters that one pigments well can dispense. The
+      Volume in microliters that one pigment well can dispense. The
       function raises an error if the total number of pixels for one
       color exceeds the content of one pigment well, i.e. if
           transfer_volume * number_pixels > well_capacity
@@ -94,13 +103,11 @@ def bioprint(image_filename, output_filename, bg_color, pigments_wells,
     quantified_image_filename
       If a path is provided, the quantified picture will be saved as an
       image file under this name.
-
     """
     pigments_wells, pigments_colors = zip(*pigments_wells.items())
 
     # Constants of the problem
-    colors = np.vstack([np.array(bg_color),
-                        np.array(pigments_colors)]).astype(float)
+    colors = np.vstack([np.array(bg_color), np.array(pigments_colors)]).astype(float)
     resolution_w, resolution_h = resolution
     resolution_ratio = 1.0 * resolution_w / resolution_h
 
@@ -125,13 +132,14 @@ def bioprint(image_filename, output_filename, bg_color, pigments_wells,
             image = image.resize(image, new_size)
     image = np.array(image)
 
-
     # QUANTIFY THE ORIGINAL IMAGE WITH THE PROVIDED PIGMENTS COLORS
 
-    image_color_distances = np.dstack([
-        ((1.0*image - color.reshape((1, 1, 3)))**2).sum(axis=2)
-        for color in colors
-    ])
+    image_color_distances = np.dstack(
+        [
+            ((1.0 * image - color.reshape((1, 1, 3))) ** 2).sum(axis=2)
+            for color in colors
+        ]
+    )
     # now image_color_distances[x,y,i] represents the distance between color
     # i and the color of the image pixel at [x,y].
     image_quantnumbers = image_color_distances.argmin(axis=2)
@@ -142,36 +150,38 @@ def bioprint(image_filename, output_filename, bg_color, pigments_wells,
     counter = Counter(image_quantnumbers.flatten())
     for color, count in counter.items():
         if (color != 0) and (count > max_pixels_per_color):
-            err_message = ("Too much pixels of color #%d. " % (color) +
-                           "Counted %d, max authorized %d" % (
-                           count, max_pixels_per_color))
+            err_message = "Too much pixels of color #%d. " % (
+                color
+            ) + "Counted %d, max authorized %d" % (count, max_pixels_per_color)
             raise ValueError(err_message)
 
     # WRITE THE CSV
     # TO DO: write the wells in an order that miminizes the Echo's travels.
-    with open(output_filename, 'w') as csvfile:
-        writer = csv.writer(csvfile, delimiter=',')
-        writer.writerow([u'Source Well',
-                         u'Destination Well',
-                         u'Transfer Volume'])
+    with open(output_filename, "w") as csvfile:
+        writer = csv.writer(csvfile, delimiter=",")
+        writer.writerow([u"Source Well", u"Destination Well", u"Transfer Volume"])
         for i, row in enumerate(image_quantnumbers):
             for j, color in enumerate(row):
                 if color != 0:
-                    writer.writerow([
-                        pigments_wells[color-1],  # source well
-                        _rownumber_to_rowname(i) + str(j+1),  # target "well"
-                        transfer_volume])
+                    writer.writerow(
+                        [
+                            pigments_wells[color - 1],  # source well
+                            _rownumber_to_rowname(i) + str(j + 1),  # target "well"
+                            transfer_volume,
+                        ]
+                    )
 
     # ESTIMATE THE PRINTING TIME
 
-    total_pixels = sum([count for (color, count) in counter.items()
-                        if color > 0])
-    print("%d pixels will be printed in appr. %.1f minutes" % (
-          total_pixels, total_pixels / transfer_rate))
+    total_pixels = sum([count for (color, count) in counter.items() if color > 0])
+    print(
+        "%d pixels will be printed in appr. %.1f minutes"
+        % (total_pixels, total_pixels / transfer_rate)
+    )
 
     # SAVE THE QUANTIFIED VERSION OF THE IMAGE IF A FILENAME IS PROVIDED
 
     if quantified_image_filename is not None:
         image_quantified = np.array([colors[y] for y in image_quantnumbers])
-        pil_image = Image.fromarray(image_quantified.astype('uint8'))
+        pil_image = Image.fromarray(image_quantified.astype("uint8"))
         pil_image.save(quantified_image_filename)

bioprinter/version.py

@@ -1 +1 @@
-__version__ = "0.1.2"
+__version__ = "0.1.3"