added GB1ECSDP plate

amygda/__init__.py

@@ -1,6 +1,7 @@
 #! /usr/bin/env python
 
 from .core import PlateMeasurement
+
 # from .statefiles import PlateMeasurementFile
 
-__version__="1.3.1"
+__version__ = "1.3.2"

bin/analyse-plate-with-amygda.py

@@ -5,53 +5,96 @@
 from scipy import stats
 
 parser = argparse.ArgumentParser()
-parser.add_argument("--image",help="the path to the image")
-parser.add_argument("--growth_pixel_threshold",default=130,type=int,help="the pixel threshold, below which a pixel is considered to be growth (0-255, default=130)")
-parser.add_argument("--growth_percentage",default=2,type=float,help="if the central measured region in a well has more than this percentage of pixels labelled as growing, then the well is classified as growth (default=2).")
-parser.add_argument("--measured_region",default=0.5,type=float,help="the radius of the central measured circle, as a decimal proportion of the whole well (default=0.5).")
-parser.add_argument("--sensitivity",default=4,type=float,help="if the average growth in the control wells is more than (sensitivity x growth_percentage), then consider growth down to this sensitivity (default=4)")
-parser.add_argument("--file_ending",default="-raw",type=str,help="the ending of the input file that is stripped. Default is '-raw' ")
-parser.add_argument("--plate_design",default="UKMYC5",type=str,help="the name of the plate design. Must have a series of matching files in config/")
+parser.add_argument("--image", help="the path to the image")
+parser.add_argument(
+    "--growth_pixel_threshold",
+    default=130,
+    type=int,
+    help="the pixel threshold, below which a pixel is considered to be growth (0-255, default=130)",
+)
+parser.add_argument(
+    "--growth_percentage",
+    default=2,
+    type=float,
+    help="if the central measured region in a well has more than this percentage of pixels labelled as growing, then the well is classified as growth (default=2).",
+)
+parser.add_argument(
+    "--measured_region",
+    default=0.5,
+    type=float,
+    help="the radius of the central measured circle, as a decimal proportion of the whole well (default=0.5).",
+)
+parser.add_argument(
+    "--sensitivity",
+    default=4,
+    type=float,
+    help="if the average growth in the control wells is more than (sensitivity x growth_percentage), then consider growth down to this sensitivity (default=4)",
+)
+parser.add_argument(
+    "--file_ending",
+    default="-raw",
+    type=str,
+    help="the ending of the input file that is stripped. Default is '-raw' ",
+)
+parser.add_argument(
+    "--plate_design",
+    default="UKMYC5",
+    type=str,
+    help="the name of the plate design. Must have a series of matching files in config/",
+)
 # parser.add_argument("--pixel_intensities",action="store_true",help="calculate and store the measured pixel intensities in the centre of each well? Default is False")
 options = parser.parse_args()
 
 # parse the path to the input image and work out its stem of
-if '/' in options.image:
-    cols=options.image.split('/')
-    image_name=cols[-1].split(options.file_ending)[0]
-    image_path=cols[0]+"/"
+if "/" in options.image:
+    cols = options.image.split("/")
+    image_name = cols[-1].split(options.file_ending)[0]
+    image_path = cols[0] + "/"
     for i in cols[1:-1]:
-        image_path+=i
-        image_path+="/"
+        image_path += i
+        image_path += "/"
 else:
-    image_path="."
-    image_name=options.image.split(options.file_ending)[0]
-
-assert options.plate_design in ['UKMYC5','UKMYC6','GPALL1F','CHNMCMM2','LeeLab'], "this plate design is not recognised"
+    image_path = "."
+    image_name = options.image.split(options.file_ending)[0]
+
+assert options.plate_design in [
+    "UKMYC5",
+    "UKMYC6",
+    "GPALL1F",
+    "CHNMCMM2",
+    "LeeLab",
+    "GB1ECSDP",
+], "this plate design is not recognised"
 
 # create a new measurement
-plate=amygda.PlateMeasurement(image_path,categories={'ImageFileName':image_name},configuration_path="config/",pixel_intensities=False,plate_design=options.plate_design)
+plate = amygda.PlateMeasurement(
+    image_path,
+    categories={"ImageFileName": image_name},
+    configuration_path="config/",
+    pixel_intensities=False,
+    plate_design=options.plate_design,
+)
 
 # create the path for the output images
-plate_stem=plate.abspath+plate.image_name
+plate_stem = plate.abspath + plate.image_name
 
 # define some colours for the output
 # the below are a contrasting set of colours taken from ColorBrewer 2
 # http://colorbrewer2.org/#type=qualitative&scheme=Dark2&n=7
 # you are, of course, free to make up your own!
 # Note these are (B,G,R) not (R,G,B)
-pink=(138,41,231)
-yellow=(51,255,255)
-teal=(119,158,27)
-green=(36,166,102)
-black=(0,0,0)
-white=(255,255,255)
+pink = (138, 41, 231)
+yellow = (51, 255, 255)
+teal = (119, 158, 27)
+green = (36, 166, 102)
+black = (0, 0, 0)
+white = (255, 255, 255)
 
 # load the raw image
 plate.load_image("-raw.png")
 
 # record that this image exists
-plate.categories['IM_IMAGE_DOWNLOADED']=True
+plate.categories["IM_IMAGE_DOWNLOADED"] = True
 
 # apply a mean shift filter to smooth the background colours
 plate.mean_shift_filter()
@@ -69,30 +112,39 @@
 plate.save_image("-filtered.jpg")
 
 # record that this image has been filtered
-plate.categories['IM_IMAGE_FILTERED']=True
+plate.categories["IM_IMAGE_FILTERED"] = True
 
 # load in the photo of the plate
 plate.load_image("-filtered.jpg")
 
 # attempt to segment the wells
-if plate.identify_wells(hough_param1=20,hough_param2=25,radius_tolerance=0.005,verbose=False):
+if plate.identify_wells(
+    hough_param1=20, hough_param2=25, radius_tolerance=0.005, verbose=False
+):
 
-    plate.categories['IM_WELLS_IDENTIFIED']=True
+    plate.categories["IM_WELLS_IDENTIFIED"] = True
 
-     # measure growth
-    plate.measure_growth(region=options.measured_region,threshold_pixel=options.growth_pixel_threshold,threshold_percentage=options.growth_percentage,sensitivity=options.sensitivity)
+    # measure growth
+    plate.measure_growth(
+        region=options.measured_region,
+        threshold_pixel=options.growth_pixel_threshold,
+        threshold_percentage=options.growth_percentage,
+        sensitivity=options.sensitivity,
+    )
 
     # save the numpy arrays containing the growth, positions of wells etc to disc
     plate.save_arrays("-arrays.npz")
 
     # draw circles around the wells
-    plate.annotate_well_circumference(color=pink,linewidth=2)
+    plate.annotate_well_circumference(color=pink, linewidth=2)
 
     # write the drug and concentration
-    plate.annotate_well_drugs_concs(color=black,fontsize=0.5)
+    plate.annotate_well_drugs_concs(color=black, fontsize=0.5)
 
     # add squares where the algorithm has detected growth
-    plate.annotate_well_analysed_region(growth_color=yellow,region=options.measured_region,thickness=3)
+    plate.annotate_well_analysed_region(
+        growth_color=yellow, region=options.measured_region, thickness=3
+    )
 
     # save the final image with wells with identified growth marked by red squares
     plate.save_image("-growth.jpg")

config/GB1ECSDP-conc-matrix.txt

@@ -0,0 +1,8 @@
+    1,     2,    2,     1, 0.25,  0.12, 0.25,    2,   0.5,   0.25,  0.06,  0.5
+    2,     4,    4,     2,  0.5,  0.25,  0.5,    4,     1,    0.5,  0.12,    1
+    4,     8,    8,     4,    1,   0.5,    1,    8,     2,      1,  0.25,    2
+    8,    16,   16,     8,    2,     1,    2,   16,     4,      2,   0.5,    4
+   16,    32,   32,    16,    4,     2,    4,   32,     8,      4,     1,    8
+   32,    64,   64,    32,    8,     4,    8,   64,    16,      8,     2,   16
+   64,   128,  128,    64,   16,     8,   16,  128,    32,     16,     4,   32
+ 0.25,   0.5,    1,     2,    4,     8,   16,   32,     0,      0,     0,    0

config/GB1ECSDP-dilution-matrix.txt

@@ -0,0 +1,8 @@
+    1,     1,    1,     1,    1,     1,    1,    1,     1,      1,     1,    1
+    2,     2,    2,     2,    2,     2,    2,    2,     2,      2,     2,    2
+    3,     3,    3,     3,    3,     3,    3,    3,     3,      3,     3,    3
+    4,     4,    4,     4,    4,     4,    4,    4,     4,      4,     4,    4
+    5,     5,    5,     5,    5,     5,    5,    5,     5,      5,     5,    5
+    6,     6,    6,     6,    6,     6,    6,    6,     6,      6,     6,    6
+    7,     7,    7,     7,    7,     7,    7,    7,     7,      7,     7,    7
+    1,     2,    3,     4,    5,     6,    7,    8,     0,      0,     0,    0

config/GB1ECSDP-drug-matrix.txt

@@ -0,0 +1,8 @@
+AMI,AUGC,AUG2,AZI,AZT,TGC,TAZ,CZA,C/T,AXO,CIP,GEN
+AMI,AUGC,AUG2,AZI,AZT,TGC,TAZ,CZA,C/T,AXO,CIP,GEN
+AMI,AUGC,AUG2,AZI,AZT,TGC,TAZ,CZA,C/T,AXO,CIP,GEN
+AMI,AUGC,AUG2,AZI,AZT,TGC,TAZ,CZA,C/T,AXO,CIP,GEN
+AMI,AUGC,AUG2,AZI,AZT,TGC,TAZ,CZA,C/T,AXO,CIP,GEN
+AMI,AUGC,AUG2,AZI,AZT,TGC,TAZ,CZA,C/T,AXO,CIP,GEN
+AMI,AUGC,AUG2,AZI,AZT,TGC,TAZ,CZA,C/T,AXO,CIP,GEN
+AZA,AZA,AZA,AZA,AZA,AZA,AZA,AZA,POS,POS,POS,NEG