From 768734fc066592e42cea6850025ca55cff09cc78 Mon Sep 17 00:00:00 2001 From: ChristianNitzsche Date: Tue, 24 Jan 2017 11:41:12 +0100 Subject: [PATCH 01/13] Add files via upload --- button.png | Bin 0 -> 2937 bytes cif2tif.py | 354 +++++++++++++++++++++++++++++++++++++++++++++++++++++ icon.png | Bin 0 -> 12095 bytes 3 files changed, 354 insertions(+) create mode 100644 button.png create mode 100644 cif2tif.py create mode 100644 icon.png diff --git a/button.png b/button.png new file mode 100644 index 0000000000000000000000000000000000000000..a911c15ff4d0b31ad0474220fa503dde9e11442b GIT binary patch literal 2937 zcmZ`*S5TAP7X4__t7t^3AOQnNC<4Yv4NXGt5Rl$NH`0+{q=+C$`2iK_HGoJEL7EVX z6cGqT5kx?G?;URb`*t7h!#-=Bz4w|mXXfmg{oFuLlbPW<0{{Tb+FA%BGV=TzbX4S1 zog`TV0Q5KA)zl2!9UTE6Xgn>=)gZ+Z)U~k#Uy4%ZP>nHAdj%23rm|Uy4&h6b7qbl1 zJ!9)A#o}UR)!7V{TTO3On;||_iHbU?$bS{gDd#q4zmf{t%^D1z`pJ5dU4L*oujIOZ z|KKev2zaVs!O>VF0xo21%v#NeRB1(S;@S?~Z}I5s%Wo!zC^6;C1^Lh%9ta{3MO*1J 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zn9w;%bdhhv(IeY{_j)gW-w%g7&W~J^iEp3w7=ahw>v5o)2#h65A$bL8cISk0AZvlI9pk$sm#voR&HUO+aYK9E?Nx~R)3yhOJ#u?`5?@R_j8Y(3(0hN-F zmNAi%g2~>2$x4esrC?BKZ0&vf{}FikIJvt7|9`>JO4KA-!1=F(uagVR%-R2uyN@?u bfY6YTx_w802E}-nTnDt(^$?Y+c2EBU{px5r literal 0 HcmV?d00001 diff --git a/cif2tif.py b/cif2tif.py new file mode 100644 index 0000000..f16b9cd --- /dev/null +++ b/cif2tif.py @@ -0,0 +1,354 @@ +from Tkinter import * +import tkFileDialog +import tkMessageBox +import bioformats +import bioformats.formatreader +import javabridge +import skimage.io +import skimage.util.montage +import math +import os +import os.path +import click +import numpy +import numpy.random +import matplotlib.pyplot as plt + + +class Stitching(Frame): + def __init__(self, parent): + Frame.__init__(self, parent) + self.parent = parent + self.initUI() + + def initUI(self): + self.parent.title("Stitching") + self.config(bg = '#F0F0F0') + self.pack(fill = BOTH, expand = 1) + self.photo=PhotoImage(file="button.png") + + self.filename = ' ' + self.dirPath = ' ' + self.n_images = 0 + self.n_channels = 0 + self.reader = 0 + + #create canvas1 + self.canvas1 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 500, height = 180) + self.canvas1.place(x=20,y=20) + + self.button1 = Button(self.canvas1, text = "Open .cif file", command = self.read_cif) + self.button1.configure(width = 18, height = 4, background = "#33B5E5") + self.button1.place(x=30,y=60) + + self.label1 = Label(self.canvas1, text="Filename", fg='blue') + self.label1.configure(width = 23, height = 2) + self.label1.place(x=288,y=20) + + self.Text1 = Text(self.canvas1, height = 2,width=26, background = "#D2D2D2") + self.Text1.config(state=DISABLED) + self.Text1.place(x=288,y=40) + + self.label2 = Label(self.canvas1, text="Number of cells", fg='blue') + self.label2.configure(width = 23, height = 2) + self.label2.place(x=288,y=70) + + self.Text2 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text2.config(state=DISABLED) + self.Text2.place(x=288,y=90) + + self.label3 = Label(self.canvas1, text="Number of channels", fg='blue') + self.label3.configure(width = 23, height = 2) + self.label3.place(x=288,y=120) + + self.Text3 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text3.config(state=DISABLED) + self.Text3.place(x=288,y=140) + + + #create canvas2 + self.canvas2 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas2.place(x=280,y=210) + + self.button4 = Button(self.canvas2, text = "Choose output directory", command = self.chooseDir) + self.button4.configure(width = 20, height = 2, background = "#33B5E5") + self.button4.place(x=28,y=10) + + self.Text4 = Text(self.canvas2, height = 2,width=26,background = "#D2D2D2") + self.Text4.config(state=DISABLED) + self.Text4.place(x=28,y=50) + + + + self.label5 = Label(self.canvas2, text="Choose channels", fg='blue') + self.label5.configure(width = 13) + self.label5.place(x=60,y=90) + + self.entry1 = Entry(self.canvas2,width = 13) + self.entry1.place(x = 60,y=108) + + self.button5 = Button(self.canvas2, image = self.photo, command = self.messageBox1, height = 30,width = 30) + self.button5.place(x=180,y=90) + + self.label6 = Label(self.canvas2, text="Grid size", fg='blue') + self.label6.configure(width = 13) + self.label6.place(x=60,y=135) + + self.entry2 = Entry(self.canvas2,width = 13) + self.entry2.place(x = 60,y=153) + + self.button6 = Button(self.canvas2, image = self.photo, command = self.messageBox2, height = 30,width = 30) + self.button6.place(x=180,y=135) + + self.button2 = Button(self.canvas2, text = "Generate tiled .tif", command = self.generate_tifs) + self.button2.configure(width = 20, height = 3, background = "#33B5E5") + self.button2.place(x=30,y=180) + + #create canvas3 + self.canvas3 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas3.place(x=20,y=210) + + self.label8 = Label(self.canvas3, text="Select cell", fg='blue') + self.label8.configure(width = 13) + self.label8.place(x=70,y=40) + + self.label9 = Label(self.canvas3, text="Select channel", fg='blue') + self.label9.configure(width = 13) + self.label9.place(x=70,y=120) + + self.entry4 = Entry(self.canvas3,width = 13) + self.entry4.place(x = 70,y=58) + + self.entry5 = Entry(self.canvas3,width= 13) + self.entry5.place(x = 70,y=138) + + self.button3 = Button(self.canvas3, text = "Display image", command = self.display_cell) + self.button3.configure(width = 20, height = 3, background = "#33B5E5") + self.button3.place(x=30,y=180) + + + def messageBox1(self): + text = "Select channel numbers. Separate each channel or range with a comma (such as 1,3,5-7). Per default all channels will be used." + tkMessageBox.showinfo("", text) + + def messageBox2(self): + text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 32 and will yield output images with 32x32 cells per montage. The maximum possible value is 100." + tkMessageBox.showinfo("", text) + + def chooseDir(self): + self.dirPath = tkFileDialog.askdirectory() + self.Text4.config(state=NORMAL) + self.Text4.delete(1.0, END) + self.Text4.insert(END,self.dirPath) + self.Text4.config(state=DISABLED) + + def read_cif(self): + old_file = self.filename + self.filename = tkFileDialog.askopenfilename() + if type(self.filename) != tuple: + if self.filename.lower().endswith('.cif'): + try: + self.Text1.config(state=NORMAL) + self.Text2.config(state=NORMAL) + self.Text3.config(state=NORMAL) + self.Text1.delete(1.0, END) + self.Text2.delete(1.0, END) + self.Text3.delete(1.0, END) + self.entry1.delete(0,END) + self.entry2.delete(0,END) + + javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') + self.reader = bioformats.formatreader.get_image_reader("tmp", path=self.filename) + self.n_images = int(0.5*javabridge.call(self.reader.metadata, "getImageCount", "()I")) + self.n_channels = javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0) + + #check, whether the .cif file is ok + if self.n_images == 0 or self.n_channels == 0: + raise ValueError('There is nothing in the file') + self.Text1.insert(END,self.filename) + self.Text1.config(state=DISABLED) + self.Text2.insert(END,self.n_images) + self.Text2.config(state=DISABLED) + self.Text3.insert(END,self.n_channels) + self.Text3.config(state=DISABLED) + self.entry1.insert(0,'1-'+str(self.n_channels)) + self.entry2.insert(0,32) + except: + tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") + if self.filename and not self.filename.lower().endswith('.cif'): + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def generate_tifs(self): + if self.reader != 0: + if type(self.dirPath) != tuple: + if os.path.isdir(self.dirPath): + output = self.dirPath + + try: + chooseChannels = self.entry1.get() + channels = [] + t = chooseChannels.split(',') + for k in t: + r = k.split('-') + for e in range(int(r[0]),int(r[-1])+1): + channels.append(e-1) + channels = list(set(channels)) + n_channels = int(javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0)) + if max(channels) < n_channels and min(channels) >= 0: + try: + grid_size = int(self.entry2.get()) + if grid_size < 1 or grid_size > 100: + raise ValueError + + self.stitch(self.reader, output,grid_size, 55, channels) + tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") + + except ValueError: + tkMessageBox.showinfo("Error", "Please enter a positive integer number between 1 and 100 as grid size.") + + else: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + except: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + else: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + else: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + else: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def display_cell(self): + flag = False + if self.reader != 0: + try: + selected_cell = int(self.entry4.get()) + selected_chan = int(self.entry5.get()) + if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: + raise ValueError + image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) + maxi = numpy.amax(image) + mini = numpy.amin(image) + ''' + f: [min,max] -> [0,255], f = m*x+n + ''' + image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) + flag = True + except: + tkMessageBox.showinfo("Error", "Please select an available cell and channel.") + if flag: + plt.imshow(image, cmap='gray') + plt.show() + + + + else: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def stitch(self,reader, output, montage_size, image_size, channels = []): + + n_images = int(0.5*javabridge.call(reader.metadata, "getImageCount", "()I")) + n_channels = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) + + chunk_size = montage_size**2 + n_chunks = self.__compute_chunks(n_images/2,montage_size) + + if len(channels) == 0: + channels = range(n_channels) + + for channel in channels: + for i in range(n_chunks): + try: + images = [reader.read(c=channel, series=image) for image in range(n_images)[::2][i*chunk_size:(i+1)*chunk_size]] + except javabridge.jutil.JavaException: + break + + images = [self.__pad_or_crop(image, image_size) for image in images] + montage = skimage.util.montage.montage2d(numpy.asarray(images), 0, grid_shape = (montage_size,montage_size)) + + if i == (n_chunks-1): + montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) + + skimage.io.imsave(os.path.join(output, "ch{:d}Im{:d}.tif".format(channel + 1,i+1)), montage) + + def __pad_or_crop(self,image, image_size): + bigger = max(image.shape[0], image.shape[1], image_size) + + pad_x = float(bigger - image.shape[0]) + pad_y = float(bigger - image.shape[1]) + + pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) + pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) + sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] + + std = numpy.std(sample) + + mean = numpy.mean(sample) + + def normal(vector, pad_width, iaxis, kwargs): + vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) + vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) + return vector + + if bigger == image_size: + return numpy.pad(image, (pad_width_x, pad_width_y), normal) + else: + if bigger == image.shape[0]: + temp_image = numpy.pad(image, (pad_width_y), normal) + else: + temp_image = numpy.pad(image, (pad_width_x), normal) + return temp_image[(bigger - image_size)/2:(bigger + image_size)/2,(bigger - image_size)/2:(bigger + image_size)/2] + + def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): + pad_x = float(montage_size*image_size - small_montage.shape[0]) + pad_y = float(montage_size*image_size - small_montage.shape[1]) + npad = ((0,int(pad_y)), (0,int(pad_x))) + return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) + + def __compute_chunks(self,n_images, montage_size): + def remainder(images, groups): + return (images - groups * (montage_size ** 2)) + + n_groups = 1 + while remainder(n_images, n_groups) > 0: + n_groups += 1 + return n_groups + + +@click.command() +@click.option("-image", type=click.Path(exists=True)) +@click.option("-output", type=click.Path(exists=False)) +@click.option("--image-size", default=55) +@click.option("--montage-size", default=30) + +def main(image,output,image_size, montage_size): + root = Tk() + root.geometry('540x470+10+50') + app = Stitching(root) + if image == None: + + root.protocol("WM_DELETE_WINDOW", on_closing) + img = PhotoImage(file='icon.png') + root.tk.call('wm', 'iconphoto', root._w, img) + app.mainloop() + else: + try: + javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') + try: + os.mkdir(output) + except: + pass + reader = bioformats.formatreader.get_image_reader("tmp", path=image) + app.stitch(reader, output, montage_size,image_size) + javabridge.kill_vm() + except: + pass + +def on_closing(): + if tkMessageBox.askokcancel("Quit", "Do you want to quit?"): + try: + javabridge.kill_vm() + finally: + quit() + +if __name__ == '__main__': + main() diff --git a/icon.png b/icon.png new file mode 100644 index 0000000000000000000000000000000000000000..b549426ea8c58cbb1fc9afd07d8cc7c0e87e18e9 GIT binary patch literal 12095 zcmb`NWl&pR6ySrq6fMOm4k=cGySo$(Qk(<`?oKJip=hDFw?HTotVmlZ?hZkV6={$H z0g5gE{k9)=c4ud2-kmqc?maW_&O7J*?u*ygRU;vMMhE}^NHo-y4FLcQrwMw zGOz#uAYg|oDd|J)?E!#5WLB25eug>i!10;%evCYYVywPW8ZSp=COMdUy5^JoUV*-f zTU;9^UqakV6>s55EL3#NkBm&k64+AnW+<(!XX zF7wG~0dK_3C^`{boE1c!1%Gm)6nfoD^EXc z_Dm1&RN+r!L^ggf6XBC_%q0^Ll99gWE3$I>VHl+qYM)#7?R0M;--G|($F0LLt6*wE 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a/cif2tif.py +++ /dev/null @@ -1,354 +0,0 @@ -from Tkinter import * -import tkFileDialog -import tkMessageBox -import bioformats -import bioformats.formatreader -import javabridge -import skimage.io -import skimage.util.montage -import math -import os -import os.path -import click -import numpy -import numpy.random -import matplotlib.pyplot as plt - - -class Stitching(Frame): - def __init__(self, parent): - Frame.__init__(self, parent) - self.parent = parent - self.initUI() - - def initUI(self): - self.parent.title("Stitching") - self.config(bg = '#F0F0F0') - self.pack(fill = BOTH, expand = 1) - self.photo=PhotoImage(file="button.png") - - self.filename = ' ' - self.dirPath = ' ' - self.n_images = 0 - self.n_channels = 0 - self.reader = 0 - - #create canvas1 - self.canvas1 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 500, height = 180) - self.canvas1.place(x=20,y=20) - - self.button1 = Button(self.canvas1, text = "Open .cif file", command = self.read_cif) - self.button1.configure(width = 18, height = 4, background = "#33B5E5") - self.button1.place(x=30,y=60) - - self.label1 = Label(self.canvas1, text="Filename", fg='blue') - self.label1.configure(width = 23, height = 2) - self.label1.place(x=288,y=20) - - self.Text1 = Text(self.canvas1, height = 2,width=26, background = "#D2D2D2") - self.Text1.config(state=DISABLED) - self.Text1.place(x=288,y=40) - - self.label2 = Label(self.canvas1, text="Number of cells", fg='blue') - self.label2.configure(width = 23, height = 2) - self.label2.place(x=288,y=70) - - self.Text2 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") - self.Text2.config(state=DISABLED) - self.Text2.place(x=288,y=90) - - self.label3 = Label(self.canvas1, text="Number of channels", fg='blue') - self.label3.configure(width = 23, height = 2) - self.label3.place(x=288,y=120) - - self.Text3 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") - self.Text3.config(state=DISABLED) - self.Text3.place(x=288,y=140) - - - #create canvas2 - self.canvas2 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) - self.canvas2.place(x=280,y=210) - - self.button4 = Button(self.canvas2, text = "Choose output directory", command = self.chooseDir) - self.button4.configure(width = 20, height = 2, background = "#33B5E5") - self.button4.place(x=28,y=10) - - self.Text4 = Text(self.canvas2, height = 2,width=26,background = "#D2D2D2") - self.Text4.config(state=DISABLED) - self.Text4.place(x=28,y=50) - - - - self.label5 = Label(self.canvas2, text="Choose channels", fg='blue') - self.label5.configure(width = 13) - self.label5.place(x=60,y=90) - - self.entry1 = Entry(self.canvas2,width = 13) - self.entry1.place(x = 60,y=108) - - self.button5 = Button(self.canvas2, image = self.photo, command = self.messageBox1, height = 30,width = 30) - self.button5.place(x=180,y=90) - - self.label6 = Label(self.canvas2, text="Grid size", fg='blue') - self.label6.configure(width = 13) - self.label6.place(x=60,y=135) - - self.entry2 = Entry(self.canvas2,width = 13) - self.entry2.place(x = 60,y=153) - - self.button6 = Button(self.canvas2, image = self.photo, command = self.messageBox2, height = 30,width = 30) - self.button6.place(x=180,y=135) - - self.button2 = Button(self.canvas2, text = "Generate tiled .tif", command = self.generate_tifs) - self.button2.configure(width = 20, height = 3, background = "#33B5E5") - self.button2.place(x=30,y=180) - - #create canvas3 - self.canvas3 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) - self.canvas3.place(x=20,y=210) - - self.label8 = Label(self.canvas3, text="Select cell", fg='blue') - self.label8.configure(width = 13) - self.label8.place(x=70,y=40) - - self.label9 = Label(self.canvas3, text="Select channel", fg='blue') - self.label9.configure(width = 13) - self.label9.place(x=70,y=120) - - self.entry4 = Entry(self.canvas3,width = 13) - self.entry4.place(x = 70,y=58) - - self.entry5 = Entry(self.canvas3,width= 13) - self.entry5.place(x = 70,y=138) - - self.button3 = Button(self.canvas3, text = "Display image", command = self.display_cell) - self.button3.configure(width = 20, height = 3, background = "#33B5E5") - self.button3.place(x=30,y=180) - - - def messageBox1(self): - text = "Select channel numbers. Separate each channel or range with a comma (such as 1,3,5-7). Per default all channels will be used." - tkMessageBox.showinfo("", text) - - def messageBox2(self): - text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 32 and will yield output images with 32x32 cells per montage. The maximum possible value is 100." - tkMessageBox.showinfo("", text) - - def chooseDir(self): - self.dirPath = tkFileDialog.askdirectory() - self.Text4.config(state=NORMAL) - self.Text4.delete(1.0, END) - self.Text4.insert(END,self.dirPath) - self.Text4.config(state=DISABLED) - - def read_cif(self): - old_file = self.filename - self.filename = tkFileDialog.askopenfilename() - if type(self.filename) != tuple: - if self.filename.lower().endswith('.cif'): - try: - self.Text1.config(state=NORMAL) - self.Text2.config(state=NORMAL) - self.Text3.config(state=NORMAL) - self.Text1.delete(1.0, END) - self.Text2.delete(1.0, END) - self.Text3.delete(1.0, END) - self.entry1.delete(0,END) - self.entry2.delete(0,END) - - javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') - self.reader = bioformats.formatreader.get_image_reader("tmp", path=self.filename) - self.n_images = int(0.5*javabridge.call(self.reader.metadata, "getImageCount", "()I")) - self.n_channels = javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0) - - #check, whether the .cif file is ok - if self.n_images == 0 or self.n_channels == 0: - raise ValueError('There is nothing in the file') - self.Text1.insert(END,self.filename) - self.Text1.config(state=DISABLED) - self.Text2.insert(END,self.n_images) - self.Text2.config(state=DISABLED) - self.Text3.insert(END,self.n_channels) - self.Text3.config(state=DISABLED) - self.entry1.insert(0,'1-'+str(self.n_channels)) - self.entry2.insert(0,32) - except: - tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") - if self.filename and not self.filename.lower().endswith('.cif'): - tkMessageBox.showinfo("Error", "Please choose a .cif file.") - - def generate_tifs(self): - if self.reader != 0: - if type(self.dirPath) != tuple: - if os.path.isdir(self.dirPath): - output = self.dirPath - - try: - chooseChannels = self.entry1.get() - channels = [] - t = chooseChannels.split(',') - for k in t: - r = k.split('-') - for e in range(int(r[0]),int(r[-1])+1): - channels.append(e-1) - channels = list(set(channels)) - n_channels = int(javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0)) - if max(channels) < n_channels and min(channels) >= 0: - try: - grid_size = int(self.entry2.get()) - if grid_size < 1 or grid_size > 100: - raise ValueError - - self.stitch(self.reader, output,grid_size, 55, channels) - tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") - - except ValueError: - tkMessageBox.showinfo("Error", "Please enter a positive integer number between 1 and 100 as grid size.") - - else: - tkMessageBox.showinfo("Error", "Please choose correct channels.") - except: - tkMessageBox.showinfo("Error", "Please choose correct channels.") - else: - tkMessageBox.showinfo("Error", "Please choose an output directory.") - else: - tkMessageBox.showinfo("Error", "Please choose an output directory.") - else: - tkMessageBox.showinfo("Error", "Please choose a .cif file.") - - def display_cell(self): - flag = False - if self.reader != 0: - try: - selected_cell = int(self.entry4.get()) - selected_chan = int(self.entry5.get()) - if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: - raise ValueError - image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) - maxi = numpy.amax(image) - mini = numpy.amin(image) - ''' - f: [min,max] -> [0,255], f = m*x+n - ''' - image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) - flag = True - except: - tkMessageBox.showinfo("Error", "Please select an available cell and channel.") - if flag: - plt.imshow(image, cmap='gray') - plt.show() - - - - else: - tkMessageBox.showinfo("Error", "Please choose a .cif file.") - - def stitch(self,reader, output, montage_size, image_size, channels = []): - - n_images = int(0.5*javabridge.call(reader.metadata, "getImageCount", "()I")) - n_channels = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) - - chunk_size = montage_size**2 - n_chunks = self.__compute_chunks(n_images/2,montage_size) - - if len(channels) == 0: - channels = range(n_channels) - - for channel in channels: - for i in range(n_chunks): - try: - images = [reader.read(c=channel, series=image) for image in range(n_images)[::2][i*chunk_size:(i+1)*chunk_size]] - except javabridge.jutil.JavaException: - break - - images = [self.__pad_or_crop(image, image_size) for image in images] - montage = skimage.util.montage.montage2d(numpy.asarray(images), 0, grid_shape = (montage_size,montage_size)) - - if i == (n_chunks-1): - montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) - - skimage.io.imsave(os.path.join(output, "ch{:d}Im{:d}.tif".format(channel + 1,i+1)), montage) - - def __pad_or_crop(self,image, image_size): - bigger = max(image.shape[0], image.shape[1], image_size) - - pad_x = float(bigger - image.shape[0]) - pad_y = float(bigger - image.shape[1]) - - pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) - pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) - sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] - - std = numpy.std(sample) - - mean = numpy.mean(sample) - - def normal(vector, pad_width, iaxis, kwargs): - vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) - vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) - return vector - - if bigger == image_size: - return numpy.pad(image, (pad_width_x, pad_width_y), normal) - else: - if bigger == image.shape[0]: - temp_image = numpy.pad(image, (pad_width_y), normal) - else: - temp_image = numpy.pad(image, (pad_width_x), normal) - return temp_image[(bigger - image_size)/2:(bigger + image_size)/2,(bigger - image_size)/2:(bigger + image_size)/2] - - def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): - pad_x = float(montage_size*image_size - small_montage.shape[0]) - pad_y = float(montage_size*image_size - small_montage.shape[1]) - npad = ((0,int(pad_y)), (0,int(pad_x))) - return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) - - def __compute_chunks(self,n_images, montage_size): - def remainder(images, groups): - return (images - groups * (montage_size ** 2)) - - n_groups = 1 - while remainder(n_images, n_groups) > 0: - n_groups += 1 - return n_groups - - -@click.command() -@click.option("-image", type=click.Path(exists=True)) -@click.option("-output", type=click.Path(exists=False)) -@click.option("--image-size", default=55) -@click.option("--montage-size", default=30) - -def main(image,output,image_size, montage_size): - root = Tk() - root.geometry('540x470+10+50') - app = Stitching(root) - if image == None: - - root.protocol("WM_DELETE_WINDOW", on_closing) - img = PhotoImage(file='icon.png') - root.tk.call('wm', 'iconphoto', root._w, img) - app.mainloop() - else: - try: - javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') - try: - os.mkdir(output) - except: - pass - reader = bioformats.formatreader.get_image_reader("tmp", path=image) - app.stitch(reader, output, montage_size,image_size) - javabridge.kill_vm() - except: - pass - -def on_closing(): - if tkMessageBox.askokcancel("Quit", "Do you want to quit?"): - try: - javabridge.kill_vm() - finally: - quit() - -if __name__ == '__main__': - main() From c8ef8005a9577b9e3f297997b975c2b9180fc3a6 Mon Sep 17 00:00:00 2001 From: ChristianNitzsche Date: Tue, 24 Jan 2017 18:41:46 +0100 Subject: [PATCH 03/13] Add files via upload --- button.png | Bin 2937 -> 2955 bytes stitching.py | 354 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 354 insertions(+) create mode 100644 stitching.py diff --git a/button.png b/button.png index a911c15ff4d0b31ad0474220fa503dde9e11442b..3863e4dea3ea24411c51726bf97b33e50bcce7d0 100644 GIT binary patch delta 376 zcmV-;0f+wi7K<0KtqC@K(*UH?0J75nxYGcu(*T~+0Cv+3cGCct(*V=c0L;?>gVO-U z(*VEI0E*L$vC{wl|6$~)Vw2+uEq@phB`4_|n2Z1b0NF`IK~yNueUjS}gCGnC8BFfm*+L=QIpxHh|oMyoDTXVg$HiS1j zGqU9T3AZj3!{s`+y(Y^QQ>kFfx3^)nm2ZQC?6uL{R(*6HvSv%NR^~u&T@(+7H(mrx z0000bbVXQnWMOn=I%9HWVUzp{3=}j}F*rIiH###pD=;xSFfiBFSD}*}3mp_RR53U@ WGdDUjIV&(RIxsM%i|-wiO$#jM^QYDT delta 341 zcmeAc|0%X%EvMOp%M42{Gjv^MD7(y1bD3fFWrqEi`GD-{ml@7nX4rI@;n-z{9hVs{ zUuI~&+_Ul0|Ns93vliT${Fqa>UYtu;OFYHs9|Hr!aZeY=5RLP-lU@onEAX^1yVxA) zaNm0Uw|%;|k z95LO9B`+p!Mr+;yn>V-YC&;wtgdGu<;oarL%CvbBgBCaIlE1H?Z&^2g=1GVB+)ux3 z&e*&5r1fOA3#+fIWuH!O7QUZ7_umP#<#X8+Yt?(N2-Y%imGTK4eKW&&@?S1l5#ta; jLn{+gD-$Da14AnVgN|*siIerXF(rP!ZoNA>o?8b1O!Sn& diff --git a/stitching.py b/stitching.py new file mode 100644 index 0000000..f16b9cd --- /dev/null +++ b/stitching.py @@ -0,0 +1,354 @@ +from Tkinter import * +import tkFileDialog +import tkMessageBox +import bioformats +import bioformats.formatreader +import javabridge +import skimage.io +import skimage.util.montage +import math +import os +import os.path +import click +import numpy +import numpy.random +import matplotlib.pyplot as plt + + +class Stitching(Frame): + def __init__(self, parent): + Frame.__init__(self, parent) + self.parent = parent + self.initUI() + + def initUI(self): + self.parent.title("Stitching") + self.config(bg = '#F0F0F0') + self.pack(fill = BOTH, expand = 1) + self.photo=PhotoImage(file="button.png") + + self.filename = ' ' + self.dirPath = ' ' + self.n_images = 0 + self.n_channels = 0 + self.reader = 0 + + #create canvas1 + self.canvas1 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 500, height = 180) + self.canvas1.place(x=20,y=20) + + self.button1 = Button(self.canvas1, text = "Open .cif file", command = self.read_cif) + self.button1.configure(width = 18, height = 4, background = "#33B5E5") + self.button1.place(x=30,y=60) + + self.label1 = Label(self.canvas1, text="Filename", fg='blue') + self.label1.configure(width = 23, height = 2) + self.label1.place(x=288,y=20) + + self.Text1 = Text(self.canvas1, height = 2,width=26, background = "#D2D2D2") + self.Text1.config(state=DISABLED) + self.Text1.place(x=288,y=40) + + self.label2 = Label(self.canvas1, text="Number of cells", fg='blue') + self.label2.configure(width = 23, height = 2) + self.label2.place(x=288,y=70) + + self.Text2 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text2.config(state=DISABLED) + self.Text2.place(x=288,y=90) + + self.label3 = Label(self.canvas1, text="Number of channels", fg='blue') + self.label3.configure(width = 23, height = 2) + self.label3.place(x=288,y=120) + + self.Text3 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text3.config(state=DISABLED) + self.Text3.place(x=288,y=140) + + + #create canvas2 + self.canvas2 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas2.place(x=280,y=210) + + self.button4 = Button(self.canvas2, text = "Choose output directory", command = self.chooseDir) + self.button4.configure(width = 20, height = 2, background = "#33B5E5") + self.button4.place(x=28,y=10) + + self.Text4 = Text(self.canvas2, height = 2,width=26,background = "#D2D2D2") + self.Text4.config(state=DISABLED) + self.Text4.place(x=28,y=50) + + + + self.label5 = Label(self.canvas2, text="Choose channels", fg='blue') + self.label5.configure(width = 13) + self.label5.place(x=60,y=90) + + self.entry1 = Entry(self.canvas2,width = 13) + self.entry1.place(x = 60,y=108) + + self.button5 = Button(self.canvas2, image = self.photo, command = self.messageBox1, height = 30,width = 30) + self.button5.place(x=180,y=90) + + self.label6 = Label(self.canvas2, text="Grid size", fg='blue') + self.label6.configure(width = 13) + self.label6.place(x=60,y=135) + + self.entry2 = Entry(self.canvas2,width = 13) + self.entry2.place(x = 60,y=153) + + self.button6 = Button(self.canvas2, image = self.photo, command = self.messageBox2, height = 30,width = 30) + self.button6.place(x=180,y=135) + + self.button2 = Button(self.canvas2, text = "Generate tiled .tif", command = self.generate_tifs) + self.button2.configure(width = 20, height = 3, background = "#33B5E5") + self.button2.place(x=30,y=180) + + #create canvas3 + self.canvas3 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas3.place(x=20,y=210) + + self.label8 = Label(self.canvas3, text="Select cell", fg='blue') + self.label8.configure(width = 13) + self.label8.place(x=70,y=40) + + self.label9 = Label(self.canvas3, text="Select channel", fg='blue') + self.label9.configure(width = 13) + self.label9.place(x=70,y=120) + + self.entry4 = Entry(self.canvas3,width = 13) + self.entry4.place(x = 70,y=58) + + self.entry5 = Entry(self.canvas3,width= 13) + self.entry5.place(x = 70,y=138) + + self.button3 = Button(self.canvas3, text = "Display image", command = self.display_cell) + self.button3.configure(width = 20, height = 3, background = "#33B5E5") + self.button3.place(x=30,y=180) + + + def messageBox1(self): + text = "Select channel numbers. Separate each channel or range with a comma (such as 1,3,5-7). Per default all channels will be used." + tkMessageBox.showinfo("", text) + + def messageBox2(self): + text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 32 and will yield output images with 32x32 cells per montage. The maximum possible value is 100." + tkMessageBox.showinfo("", text) + + def chooseDir(self): + self.dirPath = tkFileDialog.askdirectory() + self.Text4.config(state=NORMAL) + self.Text4.delete(1.0, END) + self.Text4.insert(END,self.dirPath) + self.Text4.config(state=DISABLED) + + def read_cif(self): + old_file = self.filename + self.filename = tkFileDialog.askopenfilename() + if type(self.filename) != tuple: + if self.filename.lower().endswith('.cif'): + try: + self.Text1.config(state=NORMAL) + self.Text2.config(state=NORMAL) + self.Text3.config(state=NORMAL) + self.Text1.delete(1.0, END) + self.Text2.delete(1.0, END) + self.Text3.delete(1.0, END) + self.entry1.delete(0,END) + self.entry2.delete(0,END) + + javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') + self.reader = bioformats.formatreader.get_image_reader("tmp", path=self.filename) + self.n_images = int(0.5*javabridge.call(self.reader.metadata, "getImageCount", "()I")) + self.n_channels = javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0) + + #check, whether the .cif file is ok + if self.n_images == 0 or self.n_channels == 0: + raise ValueError('There is nothing in the file') + self.Text1.insert(END,self.filename) + self.Text1.config(state=DISABLED) + self.Text2.insert(END,self.n_images) + self.Text2.config(state=DISABLED) + self.Text3.insert(END,self.n_channels) + self.Text3.config(state=DISABLED) + self.entry1.insert(0,'1-'+str(self.n_channels)) + self.entry2.insert(0,32) + except: + tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") + if self.filename and not self.filename.lower().endswith('.cif'): + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def generate_tifs(self): + if self.reader != 0: + if type(self.dirPath) != tuple: + if os.path.isdir(self.dirPath): + output = self.dirPath + + try: + chooseChannels = self.entry1.get() + channels = [] + t = chooseChannels.split(',') + for k in t: + r = k.split('-') + for e in range(int(r[0]),int(r[-1])+1): + channels.append(e-1) + channels = list(set(channels)) + n_channels = int(javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0)) + if max(channels) < n_channels and min(channels) >= 0: + try: + grid_size = int(self.entry2.get()) + if grid_size < 1 or grid_size > 100: + raise ValueError + + self.stitch(self.reader, output,grid_size, 55, channels) + tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") + + except ValueError: + tkMessageBox.showinfo("Error", "Please enter a positive integer number between 1 and 100 as grid size.") + + else: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + except: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + else: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + else: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + else: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def display_cell(self): + flag = False + if self.reader != 0: + try: + selected_cell = int(self.entry4.get()) + selected_chan = int(self.entry5.get()) + if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: + raise ValueError + image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) + maxi = numpy.amax(image) + mini = numpy.amin(image) + ''' + f: [min,max] -> [0,255], f = m*x+n + ''' + image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) + flag = True + except: + tkMessageBox.showinfo("Error", "Please select an available cell and channel.") + if flag: + plt.imshow(image, cmap='gray') + plt.show() + + + + else: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def stitch(self,reader, output, montage_size, image_size, channels = []): + + n_images = int(0.5*javabridge.call(reader.metadata, "getImageCount", "()I")) + n_channels = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) + + chunk_size = montage_size**2 + n_chunks = self.__compute_chunks(n_images/2,montage_size) + + if len(channels) == 0: + channels = range(n_channels) + + for channel in channels: + for i in range(n_chunks): + try: + images = [reader.read(c=channel, series=image) for image in range(n_images)[::2][i*chunk_size:(i+1)*chunk_size]] + except javabridge.jutil.JavaException: + break + + images = [self.__pad_or_crop(image, image_size) for image in images] + montage = skimage.util.montage.montage2d(numpy.asarray(images), 0, grid_shape = (montage_size,montage_size)) + + if i == (n_chunks-1): + montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) + + skimage.io.imsave(os.path.join(output, "ch{:d}Im{:d}.tif".format(channel + 1,i+1)), montage) + + def __pad_or_crop(self,image, image_size): + bigger = max(image.shape[0], image.shape[1], image_size) + + pad_x = float(bigger - image.shape[0]) + pad_y = float(bigger - image.shape[1]) + + pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) + pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) + sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] + + std = numpy.std(sample) + + mean = numpy.mean(sample) + + def normal(vector, pad_width, iaxis, kwargs): + vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) + vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) + return vector + + if bigger == image_size: + return numpy.pad(image, (pad_width_x, pad_width_y), normal) + else: + if bigger == image.shape[0]: + temp_image = numpy.pad(image, (pad_width_y), normal) + else: + temp_image = numpy.pad(image, (pad_width_x), normal) + return temp_image[(bigger - image_size)/2:(bigger + image_size)/2,(bigger - image_size)/2:(bigger + image_size)/2] + + def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): + pad_x = float(montage_size*image_size - small_montage.shape[0]) + pad_y = float(montage_size*image_size - small_montage.shape[1]) + npad = ((0,int(pad_y)), (0,int(pad_x))) + return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) + + def __compute_chunks(self,n_images, montage_size): + def remainder(images, groups): + return (images - groups * (montage_size ** 2)) + + n_groups = 1 + while remainder(n_images, n_groups) > 0: + n_groups += 1 + return n_groups + + +@click.command() +@click.option("-image", type=click.Path(exists=True)) +@click.option("-output", type=click.Path(exists=False)) +@click.option("--image-size", default=55) +@click.option("--montage-size", default=30) + +def main(image,output,image_size, montage_size): + root = Tk() + root.geometry('540x470+10+50') + app = Stitching(root) + if image == None: + + root.protocol("WM_DELETE_WINDOW", on_closing) + img = PhotoImage(file='icon.png') + root.tk.call('wm', 'iconphoto', root._w, img) + app.mainloop() + else: + try: + javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') + try: + os.mkdir(output) + except: + pass + reader = bioformats.formatreader.get_image_reader("tmp", path=image) + app.stitch(reader, output, montage_size,image_size) + javabridge.kill_vm() + except: + pass + +def on_closing(): + if tkMessageBox.askokcancel("Quit", "Do you want to quit?"): + try: + javabridge.kill_vm() + finally: + quit() + +if __name__ == '__main__': + main() From cf370b218d0b4fd2a3d7462b16ecc32fc83c9c15 Mon Sep 17 00:00:00 2001 From: ChristianNitzsche Date: Tue, 24 Jan 2017 18:43:35 +0100 Subject: [PATCH 04/13] Add files via upload --- README.rst | 797 ++++++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 754 insertions(+), 43 deletions(-) diff --git a/README.rst b/README.rst index 5f52cbb..c311c25 100755 --- a/README.rst +++ b/README.rst @@ -1,67 +1,778 @@ -Stitching -========= -Stitch images to form a montage. -Requirements -============ -Java development kit -Python 2.7.12 + + + + + -pip + + + + + + -numpy - $ pip install numpy + + + + + stitching/README.rst at master ยท holgerhennig/stitching + + + + + + + + + + + + + -scipy - $ pip install scipy + + + + + + + + + -click - $ pip install click + + + -skimage - $ pip install skimage + + + -python-bioformats - $ pip install python-bioformats + + -matplotlib - $ pip install matplotlib -Additional in Windows OS: Visual C++ 9.0 -Installation -============ + - $ git clone https://github.com/CellProfiler/stitching.git - $ cd /path/to/stitching - $ pip install -e . + + -Use -=== + + - $ python stitching -o path/to/OUTPUT_DIRECTORY path/to/IMAGE -Generates per-channel tiled images from IMAGE saved to OUTPUT_DIRECTORY. Each image in IMAGE has shape 55px by 55px and -is padded with random noise. Files are named "ch1.tif", "ch2.tif", ..., one for each channel. + + -Optional: + ---image-size - Set the window size of the tile images (default: --image-size 55). - If user sets a size bigger than the original images, each of the tile images will be padded with its own background. - If user sets a size smaller than the original images, each of the tile images will be cropped toward its center. ---montage-size - Set the size of the final montage (default: --montage-size 30). - If the total number of original images could not fill up the desired montage size, the montage will be padded with black background. - For example: + + - Number of total images: 1000 + + + - User setting: --image-size 20 --montage-size 30 + + + + + + + + + +
+ Skip to content + + + + + + + + + + + + + +
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+ + /stitching + + + forked from CellProfiler/stitching + +

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+ stitching/README.rst +
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+ + + 8cd6636 + + Jan 24, 2017 + + + +
+ + @minh-doan + @holgerhennig + @0x00b1 + @mcquin + + +
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+ Raw + Blame + History +
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+ 75 lines (48 sloc) + + 2.4 KB +
+
+ + +
+
+

Stitching

+

Stitch images to form a montage. A montage contains of a n-by-n grid, where in each grid compartment an image can be placed, e.g., a 5-by-5 montage contains 25 images in total. Visit http://cellprofiler.org/imagingflowcytometry/ for more information on the imaging flow cytometry workflow and the image stitching (also referred to as image tiling).

+ +

Requirements

+

Java development kit

+

Python 2.7.12

+

pip

+
+
numpy
+
$ pip install numpy
+
scipy
+
$ pip install scipy
+
click
+
$ pip install click
+
skimage
+
$ pip install skimage
+
python-bioformats
+
$ pip install python-bioformats
+
matplotlib
+
$ pip install matplotlib
+
+

Additional in Windows OS: Visual C++ 9.0

+ +

Installation

+
+

$ git clone https://github.com/CellProfiler/stitching.git

+

$ cd /path/to/stitching

+

$ pip install -e .

+
+ +

Use

+

Generates per-channel montages from IMAGE saved to OUTPUT_DIRECTORY. Each image in IMAGE has shape 55px by 55px and is padded with random noise. Montage files are named "ch1.tif", "ch2.tif", ..., one for each channel.

+

Open a new command line window (also called command prompt window in Windows OS or terminal in MAC OS). Now, to generate the montages, you can either (1) start the stitching GUI or (2) use the command line.

+
    +
  1. To use the GUI, type
    2. +
+
+$ python stitching.py
+

The GUI window will open where you can select a .cif file to generate the montages. Optionally you can also display selected images from the .cif file.

+

OR

+
    +
  1. To use the command line, type
    2. +
+
+$ python stitching -image='path/to/IMAGE' -output path/to/OUTPUT_DIRECTORY
+

Optional:

+ + + + + + + + + +
+--image-sizeSet the window size of the tile images (default: --image-size 55). +If user sets a size bigger than the original images, each of the tile images will be padded with its own background. +If user sets a size smaller than the original images, each of the tile images will be cropped toward its center.
+--montage-size

Set the size of the final montage (default: --montage-size 30). +If the total number of original images could not fill up the desired montage size, the montage will be padded with black background.

+
+

For example:

+

Number of total images: 1000

+

User setting: --image-size 20 --montage-size 30

+

The result would be 2 montages at the size of 600x600; one montage is filled up with 900 (30x30) tile images, one montage contains 100 tile images and remaining space is filled up by black background.

+
+
+ +
+
+ +
+ + + + +
+
+
+ + +
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+ + + You can't perform that action at this time. +
+ + + + + + + + + +
+ + You signed in with another tab or window. Reload to refresh your session. + You signed out in another tab or window. Reload to refresh your session. +
+ + + + - The result would be 2 montages at the size of 600x600; one montage is filled up with 900 (30x30) tile images, one montage contains 100 tile images and remaining space is filled up by black background. From 02ef07b0d631293ca33da289a6eaadb8aecaac22 Mon Sep 17 00:00:00 2001 From: Christian Nitzsche Date: Wed, 25 Jan 2017 14:32:44 +0100 Subject: [PATCH 05/13] update Readme --- README.rst | 800 ++++------------------------------------------------- 1 file changed, 50 insertions(+), 750 deletions(-) diff --git a/README.rst b/README.rst index c311c25..9362419 100755 --- a/README.rst +++ b/README.rst @@ -1,778 +1,78 @@ +Stitching +========= +Stitch images to form a montage. A montage contains of a n-by-n grid, where in each grid compartment an image can be placed, e.g., a 5-by-5 montage contains 25 images in total. Visit http://cellprofiler.org/imagingflowcytometry/ for more information on the imaging flow cytometry workflow and the image stitching (also referred to as image tiling). +Requirements +============ +Java development kit - - - - - +Python 2.7.12 - - - - - - +pip - - - - - stitching/README.rst at master ยท holgerhennig/stitching - - - - - - - - - - - - - +numpy + $ pip install numpy - - - - - - - - - +scipy + $ pip install scipy - - - +click + $ pip install click - - - +skimage + $ pip install skimage - - +Tkinter + typically included with your python distribution +python-bioformats + $ pip install python-bioformats +matplotlib + $ pip install matplotlib - +Additional in Windows OS: Visual C++ 9.0 +Installation +============ + $ git clone https://github.com/CellProfiler/stitching.git - - + $ cd /path/to/stitching - - + $ pip install -e . +Use +=== +Generates per-channel montages from IMAGE saved to OUTPUT_DIRECTORY. Each image in IMAGE has shape 55px by 55px and is padded with random noise. Montage files are named "ch1.tif", "ch2.tif", ..., one for each channel. - - +Open a new command line window (also called command prompt window in Windows OS or terminal in MAC OS). Now, to generate the montages, you can either (1) start the stitching GUI or (2) use the command line. - +1. To use the GUI, type + $ python stitching.py +The GUI window will open where you can select a .cif file to generate the montages. Optionally you can also display selected images from the .cif file. - - +OR - - - +2. To use the command line, type + $ python stitching -image='path/to/IMAGE' -output path/to/OUTPUT_DIRECTORY - - +Optional: - - +--image-size + Set the window size of the tile images (default: --image-size 55). + If user sets a size bigger than the original images, each of the tile images will be padded with its own background. + If user sets a size smaller than the original images, each of the tile images will be cropped toward its center. +--montage-size + Set the size of the final montage (default: --montage-size 30). + If the total number of original images could not fill up the desired montage size, the montage will be padded with black background. + For example: + Number of total images: 1000 - -
- Skip to content - - - - - - - - - - - - - -
- -
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    - - -
    - -
    • - -
  • -
    - -
    - -
    • -
- -

- - /stitching - - - forked from CellProfiler/stitching - -

- -
-
- - - -
-
- -
-
- - - -Permalink - - - -
- -
- - - -
- -
- - Find file - - -
-
- stitching/README.rst -
-
- - -
- - - 8cd6636 - - Jan 24, 2017 - - - -
- - @minh-doan - @holgerhennig - @0x00b1 - @mcquin - - -
- - -
- - -
-
-
- -
- Raw - Blame - History -
- - -
- -
- -
- -
- 75 lines (48 sloc) - - 2.4 KB -
-
- - -
-
-

Stitching

-

Stitch images to form a montage. A montage contains of a n-by-n grid, where in each grid compartment an image can be placed, e.g., a 5-by-5 montage contains 25 images in total. Visit http://cellprofiler.org/imagingflowcytometry/ for more information on the imaging flow cytometry workflow and the image stitching (also referred to as image tiling).

- -

Requirements

-

Java development kit

-

Python 2.7.12

-

pip

-
-
numpy
-
$ pip install numpy
-
scipy
-
$ pip install scipy
-
click
-
$ pip install click
-
skimage
-
$ pip install skimage
-
python-bioformats
-
$ pip install python-bioformats
-
matplotlib
-
$ pip install matplotlib
-
-

Additional in Windows OS: Visual C++ 9.0

- -

Installation

-
-

$ git clone https://github.com/CellProfiler/stitching.git

-

$ cd /path/to/stitching

-

$ pip install -e .

-
- -

Use

-

Generates per-channel montages from IMAGE saved to OUTPUT_DIRECTORY. Each image in IMAGE has shape 55px by 55px and is padded with random noise. Montage files are named "ch1.tif", "ch2.tif", ..., one for each channel.

-

Open a new command line window (also called command prompt window in Windows OS or terminal in MAC OS). Now, to generate the montages, you can either (1) start the stitching GUI or (2) use the command line.

-
    -
  1. To use the GUI, type
    2. -
-
-$ python stitching.py
-

The GUI window will open where you can select a .cif file to generate the montages. Optionally you can also display selected images from the .cif file.

-

OR

-
    -
  1. To use the command line, type
    2. -
-
-$ python stitching -image='path/to/IMAGE' -output path/to/OUTPUT_DIRECTORY
-

Optional:

- - - - - - - - - -
---image-sizeSet the window size of the tile images (default: --image-size 55). -If user sets a size bigger than the original images, each of the tile images will be padded with its own background. -If user sets a size smaller than the original images, each of the tile images will be cropped toward its center.
---montage-size

Set the size of the final montage (default: --montage-size 30). -If the total number of original images could not fill up the desired montage size, the montage will be padded with black background.

-
-

For example:

-

Number of total images: 1000

-

User setting: --image-size 20 --montage-size 30

-

The result would be 2 montages at the size of 600x600; one montage is filled up with 900 (30x30) tile images, one montage contains 100 tile images and remaining space is filled up by black background.

-
-
- -
-
- -
- - - - -
-
-
- - -
-
- -
- -
- -
- - - - - -
- - - You can't perform that action at this time. -
- - - - - - - - - -
- - You signed in with another tab or window. Reload to refresh your session. - You signed out in another tab or window. Reload to refresh your session. -
- - - - + User setting: --image-size 20 --montage-size 30 + The result would be 2 montages at the size of 600x600; one montage is filled up with 900 (30x30) tile images, one montage contains 100 tile images and remaining space is filled up by black background. From 2d4b2404d6fabe365601058e335ba3b7368abb9a Mon Sep 17 00:00:00 2001 From: Christian Nitzsche Date: Wed, 25 Jan 2017 15:03:02 +0100 Subject: [PATCH 06/13] update Main.py --- stitching.py | 354 --------------------------------- stitching/__main__.py | 449 ++++++++++++++++++++++++++++++++---------- 2 files changed, 344 insertions(+), 459 deletions(-) delete mode 100644 stitching.py mode change 100755 => 100644 stitching/__main__.py diff --git a/stitching.py b/stitching.py deleted file mode 100644 index f16b9cd..0000000 --- a/stitching.py +++ /dev/null @@ -1,354 +0,0 @@ -from Tkinter import * -import tkFileDialog -import tkMessageBox -import bioformats -import bioformats.formatreader -import javabridge -import skimage.io -import skimage.util.montage -import math -import os -import os.path -import click -import numpy -import numpy.random -import matplotlib.pyplot as plt - - -class Stitching(Frame): - def __init__(self, parent): - Frame.__init__(self, parent) - self.parent = parent - self.initUI() - - def initUI(self): - self.parent.title("Stitching") - self.config(bg = '#F0F0F0') - self.pack(fill = BOTH, expand = 1) - self.photo=PhotoImage(file="button.png") - - self.filename = ' ' - self.dirPath = ' ' - self.n_images = 0 - self.n_channels = 0 - self.reader = 0 - - #create canvas1 - self.canvas1 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 500, height = 180) - self.canvas1.place(x=20,y=20) - - self.button1 = Button(self.canvas1, text = "Open .cif file", command = self.read_cif) - self.button1.configure(width = 18, height = 4, background = "#33B5E5") - self.button1.place(x=30,y=60) - - self.label1 = Label(self.canvas1, text="Filename", fg='blue') - self.label1.configure(width = 23, height = 2) - self.label1.place(x=288,y=20) - - self.Text1 = Text(self.canvas1, height = 2,width=26, background = "#D2D2D2") - self.Text1.config(state=DISABLED) - self.Text1.place(x=288,y=40) - - self.label2 = Label(self.canvas1, text="Number of cells", fg='blue') - self.label2.configure(width = 23, height = 2) - self.label2.place(x=288,y=70) - - self.Text2 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") - self.Text2.config(state=DISABLED) - self.Text2.place(x=288,y=90) - - self.label3 = Label(self.canvas1, text="Number of channels", fg='blue') - self.label3.configure(width = 23, height = 2) - self.label3.place(x=288,y=120) - - self.Text3 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") - self.Text3.config(state=DISABLED) - self.Text3.place(x=288,y=140) - - - #create canvas2 - self.canvas2 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) - self.canvas2.place(x=280,y=210) - - self.button4 = Button(self.canvas2, text = "Choose output directory", command = self.chooseDir) - self.button4.configure(width = 20, height = 2, background = "#33B5E5") - self.button4.place(x=28,y=10) - - self.Text4 = Text(self.canvas2, height = 2,width=26,background = "#D2D2D2") - self.Text4.config(state=DISABLED) - self.Text4.place(x=28,y=50) - - - - self.label5 = Label(self.canvas2, text="Choose channels", fg='blue') - self.label5.configure(width = 13) - self.label5.place(x=60,y=90) - - self.entry1 = Entry(self.canvas2,width = 13) - self.entry1.place(x = 60,y=108) - - self.button5 = Button(self.canvas2, image = self.photo, command = self.messageBox1, height = 30,width = 30) - self.button5.place(x=180,y=90) - - self.label6 = Label(self.canvas2, text="Grid size", fg='blue') - self.label6.configure(width = 13) - self.label6.place(x=60,y=135) - - self.entry2 = Entry(self.canvas2,width = 13) - self.entry2.place(x = 60,y=153) - - self.button6 = Button(self.canvas2, image = self.photo, command = self.messageBox2, height = 30,width = 30) - self.button6.place(x=180,y=135) - - self.button2 = Button(self.canvas2, text = "Generate tiled .tif", command = self.generate_tifs) - self.button2.configure(width = 20, height = 3, background = "#33B5E5") - self.button2.place(x=30,y=180) - - #create canvas3 - self.canvas3 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) - self.canvas3.place(x=20,y=210) - - self.label8 = Label(self.canvas3, text="Select cell", fg='blue') - self.label8.configure(width = 13) - self.label8.place(x=70,y=40) - - self.label9 = Label(self.canvas3, text="Select channel", fg='blue') - self.label9.configure(width = 13) - self.label9.place(x=70,y=120) - - self.entry4 = Entry(self.canvas3,width = 13) - self.entry4.place(x = 70,y=58) - - self.entry5 = Entry(self.canvas3,width= 13) - self.entry5.place(x = 70,y=138) - - self.button3 = Button(self.canvas3, text = "Display image", command = self.display_cell) - self.button3.configure(width = 20, height = 3, background = "#33B5E5") - self.button3.place(x=30,y=180) - - - def messageBox1(self): - text = "Select channel numbers. Separate each channel or range with a comma (such as 1,3,5-7). Per default all channels will be used." - tkMessageBox.showinfo("", text) - - def messageBox2(self): - text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 32 and will yield output images with 32x32 cells per montage. The maximum possible value is 100." - tkMessageBox.showinfo("", text) - - def chooseDir(self): - self.dirPath = tkFileDialog.askdirectory() - self.Text4.config(state=NORMAL) - self.Text4.delete(1.0, END) - self.Text4.insert(END,self.dirPath) - self.Text4.config(state=DISABLED) - - def read_cif(self): - old_file = self.filename - self.filename = tkFileDialog.askopenfilename() - if type(self.filename) != tuple: - if self.filename.lower().endswith('.cif'): - try: - self.Text1.config(state=NORMAL) - self.Text2.config(state=NORMAL) - self.Text3.config(state=NORMAL) - self.Text1.delete(1.0, END) - self.Text2.delete(1.0, END) - self.Text3.delete(1.0, END) - self.entry1.delete(0,END) - self.entry2.delete(0,END) - - javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') - self.reader = bioformats.formatreader.get_image_reader("tmp", path=self.filename) - self.n_images = int(0.5*javabridge.call(self.reader.metadata, "getImageCount", "()I")) - self.n_channels = javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0) - - #check, whether the .cif file is ok - if self.n_images == 0 or self.n_channels == 0: - raise ValueError('There is nothing in the file') - self.Text1.insert(END,self.filename) - self.Text1.config(state=DISABLED) - self.Text2.insert(END,self.n_images) - self.Text2.config(state=DISABLED) - self.Text3.insert(END,self.n_channels) - self.Text3.config(state=DISABLED) - self.entry1.insert(0,'1-'+str(self.n_channels)) - self.entry2.insert(0,32) - except: - tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") - if self.filename and not self.filename.lower().endswith('.cif'): - tkMessageBox.showinfo("Error", "Please choose a .cif file.") - - def generate_tifs(self): - if self.reader != 0: - if type(self.dirPath) != tuple: - if os.path.isdir(self.dirPath): - output = self.dirPath - - try: - chooseChannels = self.entry1.get() - channels = [] - t = chooseChannels.split(',') - for k in t: - r = k.split('-') - for e in range(int(r[0]),int(r[-1])+1): - channels.append(e-1) - channels = list(set(channels)) - n_channels = int(javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0)) - if max(channels) < n_channels and min(channels) >= 0: - try: - grid_size = int(self.entry2.get()) - if grid_size < 1 or grid_size > 100: - raise ValueError - - self.stitch(self.reader, output,grid_size, 55, channels) - tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") - - except ValueError: - tkMessageBox.showinfo("Error", "Please enter a positive integer number between 1 and 100 as grid size.") - - else: - tkMessageBox.showinfo("Error", "Please choose correct channels.") - except: - tkMessageBox.showinfo("Error", "Please choose correct channels.") - else: - tkMessageBox.showinfo("Error", "Please choose an output directory.") - else: - tkMessageBox.showinfo("Error", "Please choose an output directory.") - else: - tkMessageBox.showinfo("Error", "Please choose a .cif file.") - - def display_cell(self): - flag = False - if self.reader != 0: - try: - selected_cell = int(self.entry4.get()) - selected_chan = int(self.entry5.get()) - if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: - raise ValueError - image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) - maxi = numpy.amax(image) - mini = numpy.amin(image) - ''' - f: [min,max] -> [0,255], f = m*x+n - ''' - image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) - flag = True - except: - tkMessageBox.showinfo("Error", "Please select an available cell and channel.") - if flag: - plt.imshow(image, cmap='gray') - plt.show() - - - - else: - tkMessageBox.showinfo("Error", "Please choose a .cif file.") - - def stitch(self,reader, output, montage_size, image_size, channels = []): - - n_images = int(0.5*javabridge.call(reader.metadata, "getImageCount", "()I")) - n_channels = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) - - chunk_size = montage_size**2 - n_chunks = self.__compute_chunks(n_images/2,montage_size) - - if len(channels) == 0: - channels = range(n_channels) - - for channel in channels: - for i in range(n_chunks): - try: - images = [reader.read(c=channel, series=image) for image in range(n_images)[::2][i*chunk_size:(i+1)*chunk_size]] - except javabridge.jutil.JavaException: - break - - images = [self.__pad_or_crop(image, image_size) for image in images] - montage = skimage.util.montage.montage2d(numpy.asarray(images), 0, grid_shape = (montage_size,montage_size)) - - if i == (n_chunks-1): - montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) - - skimage.io.imsave(os.path.join(output, "ch{:d}Im{:d}.tif".format(channel + 1,i+1)), montage) - - def __pad_or_crop(self,image, image_size): - bigger = max(image.shape[0], image.shape[1], image_size) - - pad_x = float(bigger - image.shape[0]) - pad_y = float(bigger - image.shape[1]) - - pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) - pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) - sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] - - std = numpy.std(sample) - - mean = numpy.mean(sample) - - def normal(vector, pad_width, iaxis, kwargs): - vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) - vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) - return vector - - if bigger == image_size: - return numpy.pad(image, (pad_width_x, pad_width_y), normal) - else: - if bigger == image.shape[0]: - temp_image = numpy.pad(image, (pad_width_y), normal) - else: - temp_image = numpy.pad(image, (pad_width_x), normal) - return temp_image[(bigger - image_size)/2:(bigger + image_size)/2,(bigger - image_size)/2:(bigger + image_size)/2] - - def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): - pad_x = float(montage_size*image_size - small_montage.shape[0]) - pad_y = float(montage_size*image_size - small_montage.shape[1]) - npad = ((0,int(pad_y)), (0,int(pad_x))) - return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) - - def __compute_chunks(self,n_images, montage_size): - def remainder(images, groups): - return (images - groups * (montage_size ** 2)) - - n_groups = 1 - while remainder(n_images, n_groups) > 0: - n_groups += 1 - return n_groups - - -@click.command() -@click.option("-image", type=click.Path(exists=True)) -@click.option("-output", type=click.Path(exists=False)) -@click.option("--image-size", default=55) -@click.option("--montage-size", default=30) - -def main(image,output,image_size, montage_size): - root = Tk() - root.geometry('540x470+10+50') - app = Stitching(root) - if image == None: - - root.protocol("WM_DELETE_WINDOW", on_closing) - img = PhotoImage(file='icon.png') - root.tk.call('wm', 'iconphoto', root._w, img) - app.mainloop() - else: - try: - javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') - try: - os.mkdir(output) - except: - pass - reader = bioformats.formatreader.get_image_reader("tmp", path=image) - app.stitch(reader, output, montage_size,image_size) - javabridge.kill_vm() - except: - pass - -def on_closing(): - if tkMessageBox.askokcancel("Quit", "Do you want to quit?"): - try: - javabridge.kill_vm() - finally: - quit() - -if __name__ == '__main__': - main() diff --git a/stitching/__main__.py b/stitching/__main__.py old mode 100755 new mode 100644 index 2b04743..f16b9cd --- a/stitching/__main__.py +++ b/stitching/__main__.py @@ -1,115 +1,354 @@ +from Tkinter import * +import tkFileDialog +import tkMessageBox +import bioformats +import bioformats.formatreader +import javabridge +import skimage.io +import skimage.util.montage import math import os import os.path - -import bioformats -import bioformats.formatreader import click -import javabridge -import javabridge.jutil import numpy import numpy.random -import skimage.io -import skimage.util.montage - +import matplotlib.pyplot as plt + + +class Stitching(Frame): + def __init__(self, parent): + Frame.__init__(self, parent) + self.parent = parent + self.initUI() + + def initUI(self): + self.parent.title("Stitching") + self.config(bg = '#F0F0F0') + self.pack(fill = BOTH, expand = 1) + self.photo=PhotoImage(file="button.png") + + self.filename = ' ' + self.dirPath = ' ' + self.n_images = 0 + self.n_channels = 0 + self.reader = 0 + + #create canvas1 + self.canvas1 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 500, height = 180) + self.canvas1.place(x=20,y=20) + + self.button1 = Button(self.canvas1, text = "Open .cif file", command = self.read_cif) + self.button1.configure(width = 18, height = 4, background = "#33B5E5") + self.button1.place(x=30,y=60) + + self.label1 = Label(self.canvas1, text="Filename", fg='blue') + self.label1.configure(width = 23, height = 2) + self.label1.place(x=288,y=20) + + self.Text1 = Text(self.canvas1, height = 2,width=26, background = "#D2D2D2") + self.Text1.config(state=DISABLED) + self.Text1.place(x=288,y=40) + + self.label2 = Label(self.canvas1, text="Number of cells", fg='blue') + self.label2.configure(width = 23, height = 2) + self.label2.place(x=288,y=70) + + self.Text2 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text2.config(state=DISABLED) + self.Text2.place(x=288,y=90) + + self.label3 = Label(self.canvas1, text="Number of channels", fg='blue') + self.label3.configure(width = 23, height = 2) + self.label3.place(x=288,y=120) + + self.Text3 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text3.config(state=DISABLED) + self.Text3.place(x=288,y=140) + + + #create canvas2 + self.canvas2 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas2.place(x=280,y=210) + + self.button4 = Button(self.canvas2, text = "Choose output directory", command = self.chooseDir) + self.button4.configure(width = 20, height = 2, background = "#33B5E5") + self.button4.place(x=28,y=10) + + self.Text4 = Text(self.canvas2, height = 2,width=26,background = "#D2D2D2") + self.Text4.config(state=DISABLED) + self.Text4.place(x=28,y=50) + + + + self.label5 = Label(self.canvas2, text="Choose channels", fg='blue') + self.label5.configure(width = 13) + self.label5.place(x=60,y=90) + + self.entry1 = Entry(self.canvas2,width = 13) + self.entry1.place(x = 60,y=108) + + self.button5 = Button(self.canvas2, image = self.photo, command = self.messageBox1, height = 30,width = 30) + self.button5.place(x=180,y=90) + + self.label6 = Label(self.canvas2, text="Grid size", fg='blue') + self.label6.configure(width = 13) + self.label6.place(x=60,y=135) + + self.entry2 = Entry(self.canvas2,width = 13) + self.entry2.place(x = 60,y=153) + + self.button6 = Button(self.canvas2, image = self.photo, command = self.messageBox2, height = 30,width = 30) + self.button6.place(x=180,y=135) + + self.button2 = Button(self.canvas2, text = "Generate tiled .tif", command = self.generate_tifs) + self.button2.configure(width = 20, height = 3, background = "#33B5E5") + self.button2.place(x=30,y=180) + + #create canvas3 + self.canvas3 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas3.place(x=20,y=210) + + self.label8 = Label(self.canvas3, text="Select cell", fg='blue') + self.label8.configure(width = 13) + self.label8.place(x=70,y=40) + + self.label9 = Label(self.canvas3, text="Select channel", fg='blue') + self.label9.configure(width = 13) + self.label9.place(x=70,y=120) + + self.entry4 = Entry(self.canvas3,width = 13) + self.entry4.place(x = 70,y=58) + + self.entry5 = Entry(self.canvas3,width= 13) + self.entry5.place(x = 70,y=138) + + self.button3 = Button(self.canvas3, text = "Display image", command = self.display_cell) + self.button3.configure(width = 20, height = 3, background = "#33B5E5") + self.button3.place(x=30,y=180) + + + def messageBox1(self): + text = "Select channel numbers. Separate each channel or range with a comma (such as 1,3,5-7). Per default all channels will be used." + tkMessageBox.showinfo("", text) + + def messageBox2(self): + text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 32 and will yield output images with 32x32 cells per montage. The maximum possible value is 100." + tkMessageBox.showinfo("", text) + + def chooseDir(self): + self.dirPath = tkFileDialog.askdirectory() + self.Text4.config(state=NORMAL) + self.Text4.delete(1.0, END) + self.Text4.insert(END,self.dirPath) + self.Text4.config(state=DISABLED) + + def read_cif(self): + old_file = self.filename + self.filename = tkFileDialog.askopenfilename() + if type(self.filename) != tuple: + if self.filename.lower().endswith('.cif'): + try: + self.Text1.config(state=NORMAL) + self.Text2.config(state=NORMAL) + self.Text3.config(state=NORMAL) + self.Text1.delete(1.0, END) + self.Text2.delete(1.0, END) + self.Text3.delete(1.0, END) + self.entry1.delete(0,END) + self.entry2.delete(0,END) + + javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') + self.reader = bioformats.formatreader.get_image_reader("tmp", path=self.filename) + self.n_images = int(0.5*javabridge.call(self.reader.metadata, "getImageCount", "()I")) + self.n_channels = javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0) + + #check, whether the .cif file is ok + if self.n_images == 0 or self.n_channels == 0: + raise ValueError('There is nothing in the file') + self.Text1.insert(END,self.filename) + self.Text1.config(state=DISABLED) + self.Text2.insert(END,self.n_images) + self.Text2.config(state=DISABLED) + self.Text3.insert(END,self.n_channels) + self.Text3.config(state=DISABLED) + self.entry1.insert(0,'1-'+str(self.n_channels)) + self.entry2.insert(0,32) + except: + tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") + if self.filename and not self.filename.lower().endswith('.cif'): + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def generate_tifs(self): + if self.reader != 0: + if type(self.dirPath) != tuple: + if os.path.isdir(self.dirPath): + output = self.dirPath + + try: + chooseChannels = self.entry1.get() + channels = [] + t = chooseChannels.split(',') + for k in t: + r = k.split('-') + for e in range(int(r[0]),int(r[-1])+1): + channels.append(e-1) + channels = list(set(channels)) + n_channels = int(javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0)) + if max(channels) < n_channels and min(channels) >= 0: + try: + grid_size = int(self.entry2.get()) + if grid_size < 1 or grid_size > 100: + raise ValueError + + self.stitch(self.reader, output,grid_size, 55, channels) + tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") + + except ValueError: + tkMessageBox.showinfo("Error", "Please enter a positive integer number between 1 and 100 as grid size.") + + else: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + except: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + else: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + else: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + else: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def display_cell(self): + flag = False + if self.reader != 0: + try: + selected_cell = int(self.entry4.get()) + selected_chan = int(self.entry5.get()) + if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: + raise ValueError + image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) + maxi = numpy.amax(image) + mini = numpy.amin(image) + ''' + f: [min,max] -> [0,255], f = m*x+n + ''' + image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) + flag = True + except: + tkMessageBox.showinfo("Error", "Please select an available cell and channel.") + if flag: + plt.imshow(image, cmap='gray') + plt.show() + + + + else: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + + def stitch(self,reader, output, montage_size, image_size, channels = []): + + n_images = int(0.5*javabridge.call(reader.metadata, "getImageCount", "()I")) + n_channels = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) + + chunk_size = montage_size**2 + n_chunks = self.__compute_chunks(n_images/2,montage_size) + + if len(channels) == 0: + channels = range(n_channels) + + for channel in channels: + for i in range(n_chunks): + try: + images = [reader.read(c=channel, series=image) for image in range(n_images)[::2][i*chunk_size:(i+1)*chunk_size]] + except javabridge.jutil.JavaException: + break + + images = [self.__pad_or_crop(image, image_size) for image in images] + montage = skimage.util.montage.montage2d(numpy.asarray(images), 0, grid_shape = (montage_size,montage_size)) + + if i == (n_chunks-1): + montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) + + skimage.io.imsave(os.path.join(output, "ch{:d}Im{:d}.tif".format(channel + 1,i+1)), montage) + + def __pad_or_crop(self,image, image_size): + bigger = max(image.shape[0], image.shape[1], image_size) + + pad_x = float(bigger - image.shape[0]) + pad_y = float(bigger - image.shape[1]) + + pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) + pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) + sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] + + std = numpy.std(sample) + + mean = numpy.mean(sample) + + def normal(vector, pad_width, iaxis, kwargs): + vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) + vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) + return vector + + if bigger == image_size: + return numpy.pad(image, (pad_width_x, pad_width_y), normal) + else: + if bigger == image.shape[0]: + temp_image = numpy.pad(image, (pad_width_y), normal) + else: + temp_image = numpy.pad(image, (pad_width_x), normal) + return temp_image[(bigger - image_size)/2:(bigger + image_size)/2,(bigger - image_size)/2:(bigger + image_size)/2] + + def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): + pad_x = float(montage_size*image_size - small_montage.shape[0]) + pad_y = float(montage_size*image_size - small_montage.shape[1]) + npad = ((0,int(pad_y)), (0,int(pad_x))) + return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) + + def __compute_chunks(self,n_images, montage_size): + def remainder(images, groups): + return (images - groups * (montage_size ** 2)) + + n_groups = 1 + while remainder(n_images, n_groups) > 0: + n_groups += 1 + return n_groups + @click.command() -@click.argument("image", type=click.Path(exists=True)) -@click.option("-o", "--output", type=click.Path(exists=False)) +@click.option("-image", type=click.Path(exists=True)) +@click.option("-output", type=click.Path(exists=False)) @click.option("--image-size", default=55) @click.option("--montage-size", default=30) - - -def __main__(image, output, image_size, montage_size): - try: - javabridge.start_vm(class_path=bioformats.JARS) - - os.mkdir(output) - - __stitch(image, output, image_size, montage_size) - finally: - javabridge.kill_vm() - - -def __stitch(filename, output, image_size, montage_size): - reader = bioformats.formatreader.get_image_reader("tmp", path=filename) - - image_count = javabridge.call(reader.metadata, "getImageCount", "()I") - - channel_count = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) - - n_chunks = __compute_chunks(image_count/2,montage_size) - chunk_size = montage_size**2 - - for channel in range(channel_count): - for chunk in range(n_chunks): - try: - images = [ - reader.read(c=channel, series=image) for image in range(image_count)[::2][chunk*chunk_size:(chunk+1)*chunk_size] - ] - except javabridge.jutil.JavaException: - break - - images = [__pad_or_crop(image, image_size) for image in images] - - montage = skimage.util.montage.montage2d(numpy.asarray(images), 0) - - if chunk == (n_chunks-1): - montage = __pad_to_same_chunk_size(montage, image_size, montage_size) - - skimage.io.imsave(os.path.join(output, "ch{:d}_{:d}.tif".format(channel + 1, chunk + 1)), montage) - - -def __pad_or_crop(image, image_size): - bigger = max(image.shape[0], image.shape[1], image_size) - - pad_x = float(bigger - image.shape[0]) - pad_y = float(bigger - image.shape[1]) - - pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) - pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) - sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] - - std = numpy.std(sample) - - mean = numpy.mean(sample) - - def normal(vector, pad_width, iaxis, kwargs): - vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) - vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) - return vector - - if bigger == image_size: - return numpy.pad(image, (pad_width_x, pad_width_y), normal) - else: - if bigger == image.shape[0]: - temp_image = numpy.pad(image, (pad_width_y), normal) - else: - temp_image = numpy.pad(image, (pad_width_x), normal) - return temp_image[(bigger - image_size)/2:(bigger + image_size)/2,(bigger - image_size)/2:(bigger + image_size)/2] - - -def __pad_to_same_chunk_size(small_montage, image_size, montage_size): - pad_x = float(montage_size*image_size - small_montage.shape[0]) - - pad_y = float(montage_size*image_size - small_montage.shape[1]) - - npad = ((0,int(pad_y)), (0,int(pad_x))) - - return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) - - -def __compute_chunks(n_images, montage_size): - - def remainder(images, groups): - return (images - groups * (montage_size ** 2)) - - n_groups = 1 - - while remainder(n_images, n_groups) > 0: - n_groups += 1 - - return n_groups - -if __name__ == "__main__": - __main__() + +def main(image,output,image_size, montage_size): + root = Tk() + root.geometry('540x470+10+50') + app = Stitching(root) + if image == None: + + root.protocol("WM_DELETE_WINDOW", on_closing) + img = PhotoImage(file='icon.png') + root.tk.call('wm', 'iconphoto', root._w, img) + app.mainloop() + else: + try: + javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') + try: + os.mkdir(output) + except: + pass + reader = bioformats.formatreader.get_image_reader("tmp", path=image) + app.stitch(reader, output, montage_size,image_size) + javabridge.kill_vm() + except: + pass + +def on_closing(): + if tkMessageBox.askokcancel("Quit", "Do you want to quit?"): + try: + javabridge.kill_vm() + finally: + quit() + +if __name__ == '__main__': + main() From 25e02a76e1ba74878b53b1f5059cce0dc288971d Mon Sep 17 00:00:00 2001 From: Christian Nitzsche Date: Wed, 25 Jan 2017 15:14:22 +0100 Subject: [PATCH 07/13] update Readme --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 9362419..d1ffa0f 100755 --- a/README.rst +++ b/README.rst @@ -57,7 +57,7 @@ The GUI window will open where you can select a .cif file to generate the montag OR 2. To use the command line, type - $ python stitching -image='path/to/IMAGE' -output path/to/OUTPUT_DIRECTORY + $ python stitching -image='path/to/IMAGE' -output='path/to/OUTPUT_DIRECTORY' Optional: From 106b541c4b3c0fd889f664ff64abf204a151dad0 Mon Sep 17 00:00:00 2001 From: Christian Nitzsche Date: Wed, 25 Jan 2017 15:18:12 +0100 Subject: [PATCH 08/13] update Readme --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index d1ffa0f..d4073b3 100755 --- a/README.rst +++ b/README.rst @@ -51,7 +51,7 @@ Generates per-channel montages from IMAGE saved to OUTPUT_DIRECTORY. Each image Open a new command line window (also called command prompt window in Windows OS or terminal in MAC OS). Now, to generate the montages, you can either (1) start the stitching GUI or (2) use the command line. 1. To use the GUI, type - $ python stitching.py + $ python stitching The GUI window will open where you can select a .cif file to generate the montages. Optionally you can also display selected images from the .cif file. OR From 25e2f2f0043ce81ee8bcfe1dc4a9e0b3d1e511b0 Mon Sep 17 00:00:00 2001 From: Christian Nitzsche Date: Wed, 25 Jan 2017 15:34:38 +0100 Subject: [PATCH 09/13] update main.py --- stitching/__main__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/stitching/__main__.py b/stitching/__main__.py index f16b9cd..c3c059a 100644 --- a/stitching/__main__.py +++ b/stitching/__main__.py @@ -132,7 +132,7 @@ def messageBox1(self): tkMessageBox.showinfo("", text) def messageBox2(self): - text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 32 and will yield output images with 32x32 cells per montage. The maximum possible value is 100." + text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 30 and will yield output images with 30x30 cells per montage. The maximum possible value is 100." tkMessageBox.showinfo("", text) def chooseDir(self): @@ -172,7 +172,7 @@ def read_cif(self): self.Text3.insert(END,self.n_channels) self.Text3.config(state=DISABLED) self.entry1.insert(0,'1-'+str(self.n_channels)) - self.entry2.insert(0,32) + self.entry2.insert(0,30) except: tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") if self.filename and not self.filename.lower().endswith('.cif'): From bba6567ac247bc05e38166e190fd8d471f14637c Mon Sep 17 00:00:00 2001 From: ChristianNitzsche Date: Fri, 24 Feb 2017 14:37:05 +0100 Subject: [PATCH 10/13] Delete icon.png --- icon.png | Bin 12095 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 icon.png diff --git a/icon.png b/icon.png deleted file mode 100644 index b549426ea8c58cbb1fc9afd07d8cc7c0e87e18e9..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12095 zcmb`NWl&pR6ySrq6fMOm4k=cGySo$(Qk(<`?oKJip=hDFw?HTotVmlZ?hZkV6={$H 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zx@0o>WfR#Viy{z70sJX?X_V*+a#=fBHIWifLjKT424g8suPFePEujEJ3eZFW2oxZX z0t8dogDF531)xxXFBAYv0X|WH4hoP&Nq$Q{J3DjyUFJk}p>Zf{4ccDD8?dRNuQ6XKavu-7i8FdP#hSKJbGf-2`kNfX-t2Iy`(`P-fOp`z z>jg$-3T;eRb@yaI?x|KfLFa(O9+xN5J2o_)qeEZtT?3ly_I}IuL0hfzV-+<;;_qXo zMp+)x9Hg;LyzioUxkF!Lqho!hKNh=MKR96(g%%>Z84<1KwfyaPIO0|8>0s0)#n8I< z&@PT>SBP_vD;0nn@(L<4@(MCHlq?ifA&M#x#amMH3J`hu(Glyy{}K55yLh^V{eJ=O v>AE0Q!1J#|fQuW%$~EYLr@tQnhw8~F$lesDN3q Date: Fri, 24 Feb 2017 14:59:25 +0100 Subject: [PATCH 12/13] update Readme, main.py --- README.rst | 15 +++++ button.gif | Bin 0 -> 337 bytes icon.gif | Bin 0 -> 12592 bytes stitching/__main__.py | 139 ++++++++++++++++++++++-------------------- 4 files changed, 88 insertions(+), 66 deletions(-) create mode 100644 button.gif create mode 100644 icon.gif diff --git a/README.rst b/README.rst index d4073b3..089b9f4 100755 --- a/README.rst +++ b/README.rst @@ -35,6 +35,21 @@ matplotlib Additional in Windows OS: Visual C++ 9.0 +For MacOSX users +================ + +The error " libc++abi.dylib: terminating with uncaught exception of type ..." should be noticed to MacOSX users. To solve this: + +If users have installed "pip matplotlib", there is a directory in root called ~/.matplotlib + +Create an empty file ~/.matplotlib/matplotlibrc +add the following code: +backend: TkAgg + +Further see: + +https://www.python.org/download/mac/tcltk/ + Installation ============ diff --git a/button.gif b/button.gif new file mode 100644 index 0000000000000000000000000000000000000000..08c3263f0618e842b7ba05b154aedc9a0ff744c7 GIT binary patch literal 337 zcmZ?wbhEHblwpuzXpv>Obm`Kp9hX9;UzVx4%#eTCZNlZcRhL%myJXRMxnRkqBd0HE zHD6Aedzk?!yW}#%rppXFE;FpY%rNgVL)m4%vdaw9FEd=e%y8y1L-S>ZW0x8BUuNjK z+_Ul0e;82wC+J+1npl#WqEMb$lA+-4=^MbH!vF*z2QaW6R8Z(kQs8k}CDiJ;?|tK% zEmk`WW?tFTrD55yz+FX$&%kZt4u(FSJ#CK}8(ma{<&u^xxS}=9BkR$I7z3L*o60su zguUa*X9)Nrm$+khdV^lDM4o^xD{DQAu#}iohAnryfEZu9x3rk(6mR~dnXc(`UGv+G zy%*JIFDPd84w9~CV$g8O6QQ(r}~Nv)&R-Yg|+|y literal 0 HcmV?d00001 diff --git a/icon.gif b/icon.gif new file mode 100644 index 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z6Ns6IcOFV-<``dE8R7_m1@0tZsutY)%%7AQ%!~8`*T>J=jIU7w{Yq?(xY`|!CO@Z# z%5!1>zn;+u5ymjxXhgyw5Um2E@S8g%gVXs74l`~p3xnZI#~3OFJFrBkvttfu2x?>} zncn;)njQ*c$^t>q9=0P;=?j=tD2ZbKa}7pAU0{xdPJ(aNwb8Eg3DmV&6(UDsLc&h& z=>vc<-0a+~mfpVK=50G*pgGLr!=GBpxer34?5hVu@4I*WmAUWrN-50g{=$PW$G|Ux z7v`a7f4hw%A;9{@osHN|~ubV?*t!*Lmg#`%Frf@X)hp2EoLUu>-WQ;Xd@pM9XSn+H| zVOA_kYgYG;($6K^SfyVdNpLqW)}sC?U2Z 100: raise ValueError - self.stitch(self.reader, output,grid_size, 55, channels) tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") @@ -219,28 +222,26 @@ def generate_tifs(self): def display_cell(self): flag = False - if self.reader != 0: - try: - selected_cell = int(self.entry4.get()) - selected_chan = int(self.entry5.get()) - if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: - raise ValueError - image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) - maxi = numpy.amax(image) - mini = numpy.amin(image) - ''' - f: [min,max] -> [0,255], f = m*x+n - ''' - image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) - flag = True - except: - tkMessageBox.showinfo("Error", "Please select an available cell and channel.") - if flag: - plt.imshow(image, cmap='gray') - plt.show() - - - + if self.reader == 0: + return + try: + selected_cell = int(self.entry4.get()) + selected_chan = int(self.entry5.get()) + if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: + raise ValueError + image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) + maxi = numpy.amax(image) + mini = numpy.amin(image) + ''' + f: [min,max] -> [0,255], f = m*x+n + ''' + image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) + flag = True + except: + tkMessageBox.showinfo("Error", "Please select an available cell and channel.") + if flag: + plt.imshow(image, cmap='gray') + plt.show() else: tkMessageBox.showinfo("Error", "Please choose a .cif file.") @@ -268,8 +269,16 @@ def stitch(self,reader, output, montage_size, image_size, channels = []): if i == (n_chunks-1): montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) - skimage.io.imsave(os.path.join(output, "ch{:d}Im{:d}.tif".format(channel + 1,i+1)), montage) + skimage.io.imsave(os.path.join(output, "ch{:d}_{:d}.tif".format(channel + 1,i+1)), montage) + + def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): + pad_x = float(montage_size*image_size - small_montage.shape[0]) + pad_y = float(montage_size*image_size - small_montage.shape[1]) + npad = ((0,int(pad_y)), (0,int(pad_x))) + return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) + + def __pad_or_crop(self,image, image_size): bigger = max(image.shape[0], image.shape[1], image_size) @@ -289,20 +298,18 @@ def normal(vector, pad_width, iaxis, kwargs): vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) return vector - if bigger == image_size: + if (image_size > image.shape[0]) & (image_size > image.shape[1]): return numpy.pad(image, (pad_width_x, pad_width_y), normal) else: - if bigger == image.shape[0]: + if bigger > image.shape[1]: temp_image = numpy.pad(image, (pad_width_y), normal) else: - temp_image = numpy.pad(image, (pad_width_x), normal) - return temp_image[(bigger - image_size)/2:(bigger + image_size)/2,(bigger - image_size)/2:(bigger + image_size)/2] - - def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): - pad_x = float(montage_size*image_size - small_montage.shape[0]) - pad_y = float(montage_size*image_size - small_montage.shape[1]) - npad = ((0,int(pad_y)), (0,int(pad_x))) - return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) + if bigger > image.shape[0]: + temp_image = numpy.pad(image, (pad_width_x), normal) + else: + temp_image = image + return temp_image[(temp_image.shape[0] - image_size)/2:(temp_image.shape[0] + image_size)/2,(temp_image.shape[1] - image_size)/2:(temp_image.shape[1] + image_size)/2] + def __compute_chunks(self,n_images, montage_size): def remainder(images, groups): @@ -327,7 +334,7 @@ def main(image,output,image_size, montage_size): if image == None: root.protocol("WM_DELETE_WINDOW", on_closing) - img = PhotoImage(file='icon.png') + img = PhotoImage(file='icon.gif') root.tk.call('wm', 'iconphoto', root._w, img) app.mainloop() else: From 0414f0589d109d3e2e8191170ff4361274bc1678 Mon Sep 17 00:00:00 2001 From: Christian Nitzsche Date: Wed, 8 Mar 2017 10:39:21 +0100 Subject: [PATCH 13/13] update main.py --- stitching/__main__.py | 510 +++++++++++++++++++++--------------------- 1 file changed, 259 insertions(+), 251 deletions(-) diff --git a/stitching/__main__.py b/stitching/__main__.py index f1c54de..ffa22a1 100644 --- a/stitching/__main__.py +++ b/stitching/__main__.py @@ -16,309 +16,317 @@ class Stitching(Frame): - def __init__(self, parent): - Frame.__init__(self, parent) - self.parent = parent - self.initUI() + def __init__(self, parent): + Frame.__init__(self, parent) + self.parent = parent + self.initUI() - def initUI(self): - self.parent.title("Stitching") - self.config(bg = '#F0F0F0') - self.pack(fill = BOTH, expand = 1) - self.photo=PhotoImage(file="button.gif") - - self.filename = ' ' - self.dirPath = ' ' - self.n_images = 0 - self.n_channels = 0 - self.reader = 0 + def initUI(self): + self.parent.title("Stitching") + self.config(bg = '#F0F0F0') + self.pack(fill = BOTH, expand = 1) + self.photo=PhotoImage(file="button.gif") + + self.filename = ' ' + self.dirPath = ' ' + self.n_images = 0 + self.n_channels = 0 + self.reader = 0 #create canvas1 - self.canvas1 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 500, height = 180) - self.canvas1.place(x=20,y=20) + self.canvas1 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 500, height = 180) + self.canvas1.place(x=20,y=20) - self.button1 = Button(self.canvas1, text = "Open .cif file", command = self.read_cif) - self.button1.configure(width = 18, height = 4, background = "#33B5E5") - self.button1.place(x=30,y=60) + self.button1 = Button(self.canvas1, text = "Open .cif file", command = self.read_cif) + self.button1.configure(width = 18, height = 4, background = "#33B5E5") + self.button1.place(x=30,y=60) - self.label1 = Label(self.canvas1, text="Filename", fg='blue') - self.label1.configure(width = 23, height = 2) - self.label1.place(x=288,y=20) + self.label1 = Label(self.canvas1, text="Filename", fg='blue') + self.label1.configure(width = 23, height = 2) + self.label1.place(x=288,y=20) - self.Text1 = Text(self.canvas1, height = 2,width=26, background = "#D2D2D2") - self.Text1.config(state=DISABLED) - self.Text1.place(x=288,y=40) + self.Text1 = Text(self.canvas1, height = 2,width=26, background = "#D2D2D2") + self.Text1.config(state=DISABLED) + self.Text1.place(x=288,y=40) - self.label2 = Label(self.canvas1, text="Number of cells", fg='blue') - self.label2.configure(width = 23, height = 2) - self.label2.place(x=288,y=70) + self.label2 = Label(self.canvas1, text="Number of cells", fg='blue') + self.label2.configure(width = 23, height = 2) + self.label2.place(x=288,y=70) - self.Text2 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") - self.Text2.config(state=DISABLED) - self.Text2.place(x=288,y=90) + self.Text2 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text2.config(state=DISABLED) + self.Text2.place(x=288,y=90) - self.label3 = Label(self.canvas1, text="Number of channels", fg='blue') - self.label3.configure(width = 23, height = 2) - self.label3.place(x=288,y=120) + self.label3 = Label(self.canvas1, text="Number of channels", fg='blue') + self.label3.configure(width = 23, height = 2) + self.label3.place(x=288,y=120) - self.Text3 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") - self.Text3.config(state=DISABLED) - self.Text3.place(x=288,y=140) + self.Text3 = Text(self.canvas1, height=2, width=26, background = "#D2D2D2") + self.Text3.config(state=DISABLED) + self.Text3.place(x=288,y=140) #create canvas2 - self.canvas2 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) - self.canvas2.place(x=280,y=210) + self.canvas2 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas2.place(x=280,y=210) - self.button4 = Button(self.canvas2, text = "Choose output directory", command = self.chooseDir) - self.button4.configure(width = 20, height = 2, background = "#33B5E5") - self.button4.place(x=28,y=10) + self.button4 = Button(self.canvas2, text = "Choose output directory", command = self.chooseDir) + self.button4.configure(width = 20, height = 2, background = "#33B5E5") + self.button4.place(x=28,y=10) - self.Text4 = Text(self.canvas2, height = 2,width=26,background = "#D2D2D2") - self.Text4.config(state=DISABLED) - self.Text4.place(x=28,y=50) + self.Text4 = Text(self.canvas2, height = 2,width=26,background = "#D2D2D2") + self.Text4.config(state=DISABLED) + self.Text4.place(x=28,y=50) - self.label5 = Label(self.canvas2, text="Choose channels", fg='blue') - self.label5.configure(width = 13) - self.label5.place(x=60,y=90) + self.label5 = Label(self.canvas2, text="Choose channels", fg='blue') + self.label5.configure(width = 13) + self.label5.place(x=60,y=90) - self.entry1 = Entry(self.canvas2,width = 13) - self.entry1.place(x = 60,y=108) + self.entry1 = Entry(self.canvas2,width = 13) + self.entry1.place(x = 60,y=108) - self.button5 = Button(self.canvas2, image = self.photo, command = self.messageBox1, height = 30,width = 30) - self.button5.place(x=180,y=90) + self.button5 = Button(self.canvas2, image = self.photo, command = self.messageBox1, height = 30,width = 30) + self.button5.place(x=180,y=90) - self.label6 = Label(self.canvas2, text="Grid size", fg='blue') - self.label6.configure(width = 13) - self.label6.place(x=60,y=135) + self.label6 = Label(self.canvas2, text="Grid size", fg='blue') + self.label6.configure(width = 13) + self.label6.place(x=60,y=135) - self.entry2 = Entry(self.canvas2,width = 13) - self.entry2.place(x = 60,y=153) + self.entry2 = Entry(self.canvas2,width = 13) + self.entry2.place(x = 60,y=153) - self.button6 = Button(self.canvas2, image = self.photo, command = self.messageBox2, height = 30,width = 30) - self.button6.place(x=180,y=135) + self.button6 = Button(self.canvas2, image = self.photo, command = self.messageBox2, height = 30,width = 30) + self.button6.place(x=180,y=135) - self.button2 = Button(self.canvas2, text = "Generate tiled .tif", command = self.generate_tifs) - self.button2.configure(width = 20, height = 3, background = "#33B5E5") - self.button2.place(x=30,y=180) + self.button2 = Button(self.canvas2, text = "Generate tiled .tif", command = self.generate_tifs) + self.button2.configure(width = 20, height = 3, background = "#33B5E5") + self.button2.place(x=30,y=180) #create canvas3 - self.canvas3 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) - self.canvas3.place(x=20,y=210) - - self.label8 = Label(self.canvas3, text="Select cell", fg='blue') - self.label8.configure(width = 13) - self.label8.place(x=70,y=40) - - self.label9 = Label(self.canvas3, text="Select channel", fg='blue') - self.label9.configure(width = 13) - self.label9.place(x=70,y=120) - - self.entry4 = Entry(self.canvas3,width = 13) - self.entry4.place(x = 70,y=58) - - self.entry5 = Entry(self.canvas3,width= 13) - self.entry5.place(x = 70,y=138) - - self.button3 = Button(self.canvas3, text = "Display image", command = self.display_cell) - self.button3.configure(width = 20, height = 3, background = "#33B5E5") - self.button3.place(x=30,y=180) - - - def messageBox1(self): - text = "Select channel numbers. Separate each channel or range with a comma (such as 1,3,5-7). Per default all channels will be used." - tkMessageBox.showinfo("", text) - - def messageBox2(self): - text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 30 and will yield output images with 30x30 cells per montage. The maximum possible value is 100." - tkMessageBox.showinfo("", text) - - def chooseDir(self): - self.dirPath = tkFileDialog.askdirectory() - self.Text4.config(state=NORMAL) - self.Text4.delete(1.0, END) - self.Text4.insert(END,self.dirPath) - self.Text4.config(state=DISABLED) - - def read_cif(self): - old_file = self.filename - self.filename = tkFileDialog.askopenfilename() - - if type(self.filename) == tuple: - return - - if self.filename.lower().endswith('.cif'): - try: - self.Text1.config(state=NORMAL) - self.Text2.config(state=NORMAL) - self.Text3.config(state=NORMAL) - self.Text1.delete(1.0, END) - self.Text2.delete(1.0, END) - self.Text3.delete(1.0, END) - self.entry1.delete(0,END) - self.entry2.delete(0,END) + self.canvas3 = Canvas(self, relief = FLAT, background = "#D2D2D2",width = 240, height = 240) + self.canvas3.place(x=20,y=210) + + self.label8 = Label(self.canvas3, text="Select cell", fg='blue') + self.label8.configure(width = 13) + self.label8.place(x=70,y=40) + + self.label9 = Label(self.canvas3, text="Select channel", fg='blue') + self.label9.configure(width = 13) + self.label9.place(x=70,y=120) + + self.entry4 = Entry(self.canvas3,width = 13) + self.entry4.place(x = 70,y=58) + + self.entry5 = Entry(self.canvas3,width= 13) + self.entry5.place(x = 70,y=138) + + self.button3 = Button(self.canvas3, text = "Display image", command = self.display_cell) + self.button3.configure(width = 20, height = 3, background = "#33B5E5") + self.button3.place(x=30,y=180) + + + def messageBox1(self): + text = "Select channel numbers. Separate each channel or range with a comma (such as 1,3,5-7). Per default all channels will be used." + tkMessageBox.showinfo("", text) + + def messageBox2(self): + text = "Enter the number of cells per row and per column in the output image. The default value for the grid size is 30 and will yield output images with 30x30 cells per montage. The maximum possible value is 100." + tkMessageBox.showinfo("", text) + + def chooseDir(self): + self.dirPath = tkFileDialog.askdirectory() + self.Text4.config(state=NORMAL) + self.Text4.delete(1.0, END) + self.Text4.insert(END,self.dirPath) + self.Text4.config(state=DISABLED) + + def read_cif(self): + old_file = self.filename + self.filename = tkFileDialog.askopenfilename() + + if type(self.filename) == tuple: + return + + if self.filename.lower().endswith('.cif'): + try: + self.Text1.config(state=NORMAL) + self.Text2.config(state=NORMAL) + self.Text3.config(state=NORMAL) + self.Text1.delete(1.0, END) + self.Text2.delete(1.0, END) + self.Text3.delete(1.0, END) + self.entry1.delete(0,END) + self.entry2.delete(0,END) - javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') - self.reader = bioformats.formatreader.get_image_reader("tmp", path=self.filename) - self.n_images = int(0.5*javabridge.call(self.reader.metadata, "getImageCount", "()I")) - self.n_channels = javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0) + javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='8G') + self.reader = bioformats.formatreader.get_image_reader("tmp", path=self.filename) + self.n_images = int(0.5*javabridge.call(self.reader.metadata, "getImageCount", "()I")) + self.n_channels = javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0) - #check, whether the .cif file is ok - if self.n_images == 0 or self.n_channels == 0: - raise ValueError('There is nothing in the file') - self.Text1.insert(END,self.filename) - self.Text1.config(state=DISABLED) - self.Text2.insert(END,self.n_images) - self.Text2.config(state=DISABLED) - self.Text3.insert(END,self.n_channels) - self.Text3.config(state=DISABLED) - self.entry1.insert(0,'1-'+str(self.n_channels)) - self.entry2.insert(0,30) - except: - tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") - - if self.filename and not self.filename.lower().endswith('.cif'): - tkMessageBox.showinfo("Error", "Please choose a .cif file.") + if self.n_images == 0 or self.n_channels == 0: + raise ValueError('There is nothing in the file') + self.Text1.insert(END,self.filename) + self.Text1.config(state=DISABLED) + self.Text2.insert(END,self.n_images) + self.Text2.config(state=DISABLED) + self.Text3.insert(END,self.n_channels) + self.Text3.config(state=DISABLED) + self.entry1.insert(0,'1-'+str(self.n_channels)) + self.entry2.insert(0,30) + except: + tkMessageBox.showinfo("Error", "Please choose a correct .cif file.") + + if self.filename and not self.filename.lower().endswith('.cif'): + tkMessageBox.showinfo("Error", "Please choose a .cif file.") - def generate_tifs(self): - if self.reader != 0: - if type(self.dirPath) != tuple: - if os.path.isdir(self.dirPath): - output = self.dirPath + def generate_tifs(self): + if self.reader == 0: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + return + + if type(self.dirPath) == tuple: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + return + + + if os.path.isdir(self.dirPath): + output = self.dirPath + else: + tkMessageBox.showinfo("Error", "Please choose an output directory.") + return - try: - chooseChannels = self.entry1.get() - channels = [] - t = chooseChannels.split(',') - for k in t: - r = k.split('-') - for e in range(int(r[0]),int(r[-1])+1): - channels.append(e-1) - channels = list(set(channels)) - n_channels = int(javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0)) - if max(channels) < n_channels and min(channels) >= 0: - try: - grid_size = int(self.entry2.get()) - if grid_size < 1 or grid_size > 100: - raise ValueError - self.stitch(self.reader, output,grid_size, 55, channels) - tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") - - except ValueError: - tkMessageBox.showinfo("Error", "Please enter a positive integer number between 1 and 100 as grid size.") + try: + chooseChannels = self.entry1.get() + channels = [] + t = chooseChannels.split(',') + for k in t: + r = k.split('-') + for e in range(int(r[0]),int(r[-1])+1): + channels.append(e-1) + channels = list(set(channels)) + n_channels = int(javabridge.call(self.reader.metadata, "getChannelCount", "(I)I", 0)) + if max(channels) < n_channels and min(channels) >= 0: + try: + grid_size = int(self.entry2.get()) + if grid_size < 1 or grid_size > 100: + raise ValueError + self.stitch(self.reader, output,grid_size, 55, channels) + tkMessageBox.showinfo("", "Tiled .tif images successfully generated.") + except ValueError: + tkMessageBox.showinfo("Error", "Please enter a positive integer number between 1 and 100 as grid size.") + return - else: - tkMessageBox.showinfo("Error", "Please choose correct channels.") - except: - tkMessageBox.showinfo("Error", "Please choose correct channels.") - else: - tkMessageBox.showinfo("Error", "Please choose an output directory.") - else: - tkMessageBox.showinfo("Error", "Please choose an output directory.") - else: - tkMessageBox.showinfo("Error", "Please choose a .cif file.") - - def display_cell(self): - flag = False - if self.reader == 0: - return - try: - selected_cell = int(self.entry4.get()) - selected_chan = int(self.entry5.get()) - if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: - raise ValueError - image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) - maxi = numpy.amax(image) - mini = numpy.amin(image) - ''' - f: [min,max] -> [0,255], f = m*x+n - ''' - image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) - flag = True - except: - tkMessageBox.showinfo("Error", "Please select an available cell and channel.") - if flag: - plt.imshow(image, cmap='gray') - plt.show() - else: - tkMessageBox.showinfo("Error", "Please choose a .cif file.") + else: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + return + except: + tkMessageBox.showinfo("Error", "Please choose correct channels.") + + + + def display_cell(self): + flag = False + if self.reader == 0: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") + return + try: + selected_cell = int(self.entry4.get()) + selected_chan = int(self.entry5.get()) + if selected_cell < 1 or selected_cell > self.n_images or selected_chan < 1 or selected_chan > self.n_channels: + raise ValueError + image = self.__pad_or_crop(self.reader.read(c=selected_chan-1, series=2*(selected_cell-1)), 55) + maxi = numpy.amax(image) + mini = numpy.amin(image) + ''' + f: [min,max] -> [0,255], f = m*x+n + ''' + image = (255.0/(maxi-mini))*image - 255*mini/(maxi-mini) + flag = True + except: + tkMessageBox.showinfo("Error", "Please select an available cell and channel.") + return + if flag: + plt.imshow(image, cmap='gray') + plt.show() + else: + tkMessageBox.showinfo("Error", "Please choose a .cif file.") - def stitch(self,reader, output, montage_size, image_size, channels = []): + def stitch(self,reader, output, montage_size, image_size, channels = []): - n_images = int(0.5*javabridge.call(reader.metadata, "getImageCount", "()I")) - n_channels = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) + n_images = int(0.5*javabridge.call(reader.metadata, "getImageCount", "()I")) + n_channels = javabridge.call(reader.metadata, "getChannelCount", "(I)I", 0) - chunk_size = montage_size**2 - n_chunks = self.__compute_chunks(n_images/2,montage_size) + chunk_size = montage_size**2 + n_chunks = self.__compute_chunks(n_images/2,montage_size) - if len(channels) == 0: - channels = range(n_channels) + if len(channels) == 0: + channels = range(n_channels) - for channel in channels: - for i in range(n_chunks): - try: - images = [reader.read(c=channel, series=image) for image in range(n_images)[::2][i*chunk_size:(i+1)*chunk_size]] - except javabridge.jutil.JavaException: - break + for channel in channels: + for i in range(n_chunks): + try: + images = [reader.read(c=channel, series=image) for image in range(n_images)[::2][i*chunk_size:(i+1)*chunk_size]] + except javabridge.jutil.JavaException: + break - images = [self.__pad_or_crop(image, image_size) for image in images] - montage = skimage.util.montage.montage2d(numpy.asarray(images), 0, grid_shape = (montage_size,montage_size)) + images = [self.__pad_or_crop(image, image_size) for image in images] + montage = skimage.util.montage.montage2d(numpy.asarray(images), 0, grid_shape = (montage_size,montage_size)) - if i == (n_chunks-1): - montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) + if i == (n_chunks-1): + montage = self.__pad_to_same_chunk_size(montage, image_size, montage_size) - skimage.io.imsave(os.path.join(output, "ch{:d}_{:d}.tif".format(channel + 1,i+1)), montage) + skimage.io.imsave(os.path.join(output, "ch{:d}_{:d}.tif".format(channel + 1,i+1)), montage) - def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): - pad_x = float(montage_size*image_size - small_montage.shape[0]) - pad_y = float(montage_size*image_size - small_montage.shape[1]) - npad = ((0,int(pad_y)), (0,int(pad_x))) - return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) + def __pad_to_same_chunk_size(self,small_montage, image_size, montage_size): + pad_x = float(montage_size*image_size - small_montage.shape[0]) + pad_y = float(montage_size*image_size - small_montage.shape[1]) + npad = ((0,int(pad_y)), (0,int(pad_x))) + return numpy.pad(small_montage, pad_width=npad, mode='constant', constant_values=0) - def __pad_or_crop(self,image, image_size): - bigger = max(image.shape[0], image.shape[1], image_size) + def __pad_or_crop(self,image, image_size): + bigger = max(image.shape[0], image.shape[1], image_size) - pad_x = float(bigger - image.shape[0]) - pad_y = float(bigger - image.shape[1]) + pad_x = float(bigger - image.shape[0]) + pad_y = float(bigger - image.shape[1]) - pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) - pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) - sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] + pad_width_x = (int(math.floor(pad_x / 2)), int(math.ceil(pad_x / 2))) + pad_width_y = (int(math.floor(pad_y / 2)), int(math.ceil(pad_y / 2))) + sample = image[image.shape[0]/2-4:image.shape[0]/2+4, :8] - std = numpy.std(sample) + std = numpy.std(sample) - mean = numpy.mean(sample) + mean = numpy.mean(sample) - def normal(vector, pad_width, iaxis, kwargs): - vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) - vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) - return vector + def normal(vector, pad_width, iaxis, kwargs): + vector[:pad_width[0]] = numpy.random.normal(mean, std, vector[:pad_width[0]].shape) + vector[-pad_width[1]:] = numpy.random.normal(mean, std, vector[-pad_width[1]:].shape) + return vector - if (image_size > image.shape[0]) & (image_size > image.shape[1]): - return numpy.pad(image, (pad_width_x, pad_width_y), normal) - else: - if bigger > image.shape[1]: - temp_image = numpy.pad(image, (pad_width_y), normal) - else: - if bigger > image.shape[0]: - temp_image = numpy.pad(image, (pad_width_x), normal) - else: - temp_image = image - return temp_image[(temp_image.shape[0] - image_size)/2:(temp_image.shape[0] + image_size)/2,(temp_image.shape[1] - image_size)/2:(temp_image.shape[1] + image_size)/2] + if (image_size > image.shape[0]) & (image_size > image.shape[1]): + return numpy.pad(image, (pad_width_x, pad_width_y), normal) + else: + if bigger > image.shape[1]: + temp_image = numpy.pad(image, (pad_width_y), normal) + else: + if bigger > image.shape[0]: + temp_image = numpy.pad(image, (pad_width_x), normal) + else: + temp_image = image + return temp_image[(temp_image.shape[0] - image_size)/2:(temp_image.shape[0] + image_size)/2,(temp_image.shape[1] - image_size)/2:(temp_image.shape[1] + image_size)/2] - def __compute_chunks(self,n_images, montage_size): - def remainder(images, groups): - return (images - groups * (montage_size ** 2)) + def __compute_chunks(self,n_images, montage_size): + def remainder(images, groups): + return (images - groups * (montage_size ** 2)) - n_groups = 1 - while remainder(n_images, n_groups) > 0: - n_groups += 1 - return n_groups + n_groups = 1 + while remainder(n_images, n_groups) > 0: + n_groups += 1 + return n_groups @click.command()