changeset 0:d78372040976 draft default tip

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
author imgteam
date Wed, 21 Jul 2021 19:59:00 +0000
parents
children
files spot_detection_2d.py spot_detection_2d.xml test-data/spots_detected.tsv test-data/test_img1.tif
diffstat 4 files changed, 602 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spot_detection_2d.py	Wed Jul 21 19:59:00 2021 +0000
@@ -0,0 +1,86 @@
+"""
+Copyright 2021 Biomedical Computer Vision Group, Heidelberg University.
+Author: Qi Gao (qi.gao@bioquant.uni-heidelberg.de)
+
+Distributed under the MIT license.
+See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
+
+"""
+
+import argparse
+
+import imageio
+import numpy as np
+import pandas as pd
+from skimage.feature import peak_local_max
+from skimage.filters import gaussian
+
+
+def getbr(xy, img, nb, firstn):
+    ndata = xy.shape[0]
+    br = np.empty((ndata, 1))
+    for j in range(ndata):
+        br[j] = np.NaN
+        if not np.isnan(xy[j, 0]):
+            timg = img[xy[j, 1] - nb - 1:xy[j, 1] + nb, xy[j, 0] - nb - 1:xy[j, 0] + nb]
+            br[j] = np.mean(np.sort(timg, axis=None)[-firstn:])
+    return br
+
+
+def spot_detection(fn_in, fn_out, frame_1st=1, frame_end=0, typ_br='smoothed', th=10, ssig=1, bd=10):
+    ims_ori = imageio.mimread(fn_in, format='TIFF')
+    ims_smd = np.zeros((len(ims_ori), ims_ori[0].shape[0], ims_ori[0].shape[1]), dtype='float64')
+    if frame_end == 0 or frame_end > len(ims_ori):
+        frame_end = len(ims_ori)
+
+    for i in range(frame_1st - 1, frame_end):
+        ims_smd[i, :, :] = gaussian(ims_ori[i].astype('float64'), sigma=ssig)
+    ims_smd_max = np.max(ims_smd)
+
+    txyb_all = np.array([]).reshape(0, 4)
+    for i in range(frame_1st - 1, frame_end):
+        tmp = np.copy(ims_smd[i, :, :])
+        tmp[tmp < th * ims_smd_max / 100] = 0
+        coords = peak_local_max(tmp, min_distance=1)
+        idx_to_del = np.where((coords[:, 0] <= bd) | (coords[:, 0] >= tmp.shape[0] - bd) |
+                              (coords[:, 1] <= bd) | (coords[:, 1] >= tmp.shape[1] - bd))
+        coords = np.delete(coords, idx_to_del[0], axis=0)
+        xys = coords[:, ::-1]
+
+        if typ_br == 'smoothed':
+            intens = getbr(xys, ims_smd[i, :, :], 0, 1)
+        elif typ_br == 'robust':
+            intens = getbr(xys, ims_ori[i], 1, 4)
+        else:
+            intens = getbr(xys, ims_ori[i], 0, 1)
+
+        txyb = np.concatenate(((i + 1) * np.ones((xys.shape[0], 1)), xys, intens), axis=1)
+        txyb_all = np.concatenate((txyb_all, txyb), axis=0)
+
+    df = pd.DataFrame()
+    df['FRAME'] = txyb_all[:, 0].astype(int)
+    df['POS_X'] = txyb_all[:, 1].astype(int)
+    df['POS_Y'] = txyb_all[:, 2].astype(int)
+    df['INTENSITY'] = txyb_all[:, 3]
+    df.to_csv(fn_out, index=False, float_format='%.2f', sep="\t")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Spot detection based on local maxima")
+    parser.add_argument("fn_in", help="Name of input image sequence (stack)")
+    parser.add_argument("fn_out", help="Name of output file to save the coordinates and intensities of detected spots")
+    parser.add_argument("frame_1st", type=int, help="Index for the starting frame to detect spots (1 for first frame of the stack)")
+    parser.add_argument("frame_end", type=int, help="Index for the last frame to detect spots (0 for the last frame of the stack)")
+    parser.add_argument("typ_intens", help="smoothed or robust (for measuring the intensities of spots)")
+    parser.add_argument("thres", type=float, help="Percentage of the global maximal intensity for thresholding candidate spots")
+    parser.add_argument("ssig", type=float, help="Sigma of the Gaussian filter for noise suppression")
+    parser.add_argument("bndy", type=int, help="Number of pixels (Spots close to image boundaries will be ignored)")
+    args = parser.parse_args()
+    spot_detection(args.fn_in,
+                   args.fn_out,
+                   frame_1st=args.frame_1st,
+                   frame_end=args.frame_end,
+                   typ_br=args.typ_intens,
+                   th=args.thres,
+                   ssig=args.ssig,
+                   bd=args.bndy)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spot_detection_2d.xml	Wed Jul 21 19:59:00 2021 +0000
@@ -0,0 +1,54 @@
+<tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.1" profile="20.05"> 
+    <description>based on local intensity maxima</description>
+    <requirements>
+        <requirement type="package" version="2.9.0">imageio</requirement>
+        <requirement type="package" version="1.20.2">numpy</requirement>
+        <requirement type="package" version="1.2.4">pandas</requirement>
+        <requirement type="package" version="0.18.1">scikit-image</requirement>
+    </requirements>
+    <command>
+    <![CDATA[
+         python '$__tool_directory__/spot_detection_2d.py'
+         '$fn_in'
+         '$fn_out'
+         '$frame_1st'
+         '$frame_end'
+         '$typ_intens'
+         '$thres'
+         '$ssig'
+         '$bndy'
+    ]]>
+    </command>
+    <inputs>
+        <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" />
+        <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
+        <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
+        <param name="typ_intens" type="select" label="How to measure the intensities">
+            <option value="smoothed" selected="True">Smoothed</option>
+            <option value="robust">Robust</option>
+        </param>
+        <param name="thres" type="float" value="10" label="Percentage of the global maximal intensity as the threshold for candidate spots" />
+        <param name="ssig" type="float" value="1" label="Sigma of the Gaussian filter for noise suppression" />
+        <param name="bndy" type="integer" value="10" label="Number of pixels (Spots within n-pixel image boundaries will be ignored)" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="fn_out" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fn_in" value="test_img1.tif"/>
+            <param name="frame_1st" value="1"/>
+            <param name="frame_end" value="0"/>
+            <param name="typ_intens" value="smoothed"/>
+            <param name="thres" value="10"/>
+            <param name="ssig" value="1"/>
+            <param name="bndy" value="10"/>
+            <output name="fn_out" value="spots_detected.tsv" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    This tool detects spots and measures the intensities in a 2D image sequence based on local intensity maxima.
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spots_detected.tsv	Wed Jul 21 19:59:00 2021 +0000
@@ -0,0 +1,462 @@
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Binary file test-data/test_img1.tif has changed