Fix adv2_microarray

modules/adv2_microarray.md

@@ -4,14 +4,14 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.10.3
+    jupytext_version: 1.11.2
 kernelspec:
   display_name: Python 3
   language: python
   name: python3
 ---
 
-```{code-cell} python
+```{code-cell} ipython3
 from __future__ import division, print_function
 %matplotlib inline
 ```
@@ -46,17 +46,15 @@ More example data:
 
 - [MicroArray Genome Imaging & Clustering Tool](http://www.bio.davidson.edu/projects/MAGIC/MAGIC.html) by Laurie Heyer & team, Davidson College
 
-
-
-```{code-cell} python
+```{code-cell} ipython3
 import matplotlib.pyplot as plt
 
 import numpy as np
 
 from skimage import io, img_as_float
 ```
 
-```{code-cell} python
+```{code-cell} ipython3
 microarray = io.imread('../images/microarray.jpg')
 
 # Scale between zero and one
@@ -66,7 +64,7 @@ plt.figure(figsize=(10, 5))
 plt.imshow(microarray[:500, :1000], cmap='gray', interpolation='nearest');
 ```
 
-```{code-cell} python
+```{code-cell} ipython3
 from skimage import color
 f, (ax0, ax1) = plt.subplots(1, 2, figsize=(15, 10))
 
@@ -84,14 +82,14 @@ ax1.imshow(red_rgb, interpolation='nearest')
 plt.suptitle('\n\nPseudocolor plots of red and green channels', fontsize=16);
 ```
 
-```{code-cell} python
-from skimage import filter as filters
+```{code-cell} ipython3
+from skimage import filters
 
 mask = (green > 0.1)
 plt.imshow(mask[:1000, :1000], cmap='gray');
 ```
 
-```{code-cell} python
+```{code-cell} ipython3
 z = red.copy()
 z /= green
 z[~mask] = 0
@@ -103,26 +101,26 @@ plt.imshow(z[:500, :500], cmap=plt.cm.gray, vmin=0, vmax=2);
 
 ### Locating the grid
 
-```{code-cell} python
+```{code-cell} ipython3
 both = (green + red)
 
 plt.imshow(both, cmap='gray');
 ```
 
-```{code-cell} python
+```{code-cell} ipython3
 from skimage import feature
 
 sum_down_columns = both.sum(axis=0)
 sum_across_rows = both.sum(axis=1)
 
-dips_columns = feature.peak_local_max(sum_down_columns.max() - sum_down_columns)
-dips_columns = dips_columns.ravel()
+dips_columns = feature.peak_local_max(sum_down_columns.max() - sum_down_columns, min_distance=5)
+dips_columns = np.sort(dips_columns.ravel())
 
 M = len(dips_columns)
 column_distance = np.mean(np.diff(dips_columns))
 
-dips_rows = feature.peak_local_max(sum_across_rows.max() - sum_across_rows)
-dips_rows = dips_rows.ravel()
+dips_rows = feature.peak_local_max(sum_across_rows.max() - sum_across_rows, min_distance=5)
+dips_rows = np.sort(dips_rows.ravel())
 
 N = len(dips_rows)
 row_distance = np.mean(np.diff(dips_rows))
@@ -143,7 +141,7 @@ ax1.set_xlim(0, 200)
 ax0.set_title('Row gaps');
 ```
 
-```{code-cell} python
+```{code-cell} ipython3
 P, Q = 500, 500
 
 plt.figure(figsize=(15, 10))
@@ -158,17 +156,18 @@ for j in dips_columns[dips_columns < Q]:
 plt.axis('image');
 ```
 
-```{code-cell} python
+```{code-cell} ipython3
 out = np.zeros(microarray.shape[:2])
+M, N = len(dips_rows), len(dips_columns)
 
 for i in range(M - 1):
     for j in range(N - 1):
         row0, row1 = dips_rows[i], dips_rows[i + 1]
         col0, col1 = dips_columns[j], dips_columns[j + 1]
-        
+
         r = microarray[row0:row1, col0:col1, 0]
         g = microarray[row0:row1, col0:col1, 1]
-        
+
         ratio = r / g
         mask = ~np.isinf(ratio)
 
@@ -179,7 +178,7 @@ for i in range(M - 1):
         out[row0:row1, col0:col1] = mean_ratio
 ```
 
-```{code-cell} python
+```{code-cell} ipython3
 f, (ax0, ax1) = plt.subplots(1, 2, figsize=(15, 10))
 
 ax0.imshow(microarray)
@@ -191,21 +190,14 @@ ax1.grid(color='magenta', linewidth=1)
 
 ### Transform the intensity to spot outliers
 
-```{code-cell} python
+```{code-cell} ipython3
+from skimage import exposure
+
 f, (ax0, ax1) = plt.subplots(1, 2, figsize=(15, 10))
 
 ax0.imshow(microarray)
 ax0.grid(color='magenta', linewidth=1)
 
-ax1.imshow(np.log(0.5 + out), cmap='gray', interpolation='nearest', vmin=0, vmax=3);
+ax1.imshow(exposure.adjust_log(out, gain=0.4), cmap='gray', interpolation='nearest', vmin=0, vmax=3);
 ax1.grid(color='magenta', linewidth=1)
 ```
-
----
-
-<div style="height: 400px;"></div>
-
-```{code-cell} python
-%reload_ext load_style
-%load_style ../themes/tutorial.css
-```