Add sample and mpeg command (#24)

README.md

@@ -37,13 +37,15 @@ pip install hotaru
 
 ### Demonstration
 ```shell
-cd sample
-python make.py
-hotaru --tag default trial
-hotaru --tag d12 trial
+hotaru sample --outdir mysample
+cd mysample
+hotaru config
+# edit mysample/hotaru.ini if you need
+hotaru trial
 hotaru auto
-python mpeg.py d12
+hotaru mpeg --has-truth
 ```
+- see `mysample/hotaru/figure/`
 
 [Sample Video](https://drive.google.com/file/d/12jl1YTZDuNAq94ciJ-_Cj5tBcKmCqgRH)
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hotaru"
-version = "4.0.0"
+version = "4.0.1"
 description = "High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse"
 license = "GPL-3.0-only"
 authors = ["TAKEKAWA Takashi <[email protected]>"]

src/hotaru/console/config.py

@@ -0,0 +1,12 @@
+import pkgutil
+
+import click
+
+
+@click.command()
+def config():
+    '''Make hotaru.ini'''
+
+    data = pkgutil.get_data('hotaru.console', 'hotaru.ini').decode('utf-8')
+    with open('hotaru.ini', 'w') as f:
+        f.write(data)

src/hotaru/console/hotaru.ini

@@ -1,6 +1,20 @@
+[main]
+tag = default
+
+[default]
+
+[radius32]
+data_tag = default
+radius_max = 32.0
+
+[distance12]
+data_tag = default
+find_tag = default
+distance = 1.2
+
+
 [DEFAULT]
 workdir = hotaru
-tag = default
 data_tag =
 find_tag =
 init_tag =
@@ -36,8 +50,3 @@ epoch = 100
 steps = 100
 batch = 100
 window = 100
-
-[main]
-tag = default
-
-[default]

src/hotaru/console/main.py

@@ -4,6 +4,7 @@
 import click
 
 from .obj import Obj
+from .config import config
 from .run.data import data
 from .run.find import find
 from .run.init import init
@@ -14,6 +15,8 @@
 from .trial import trial
 from .auto import auto
 from .figure import figure
+from .mpeg import mpeg
+from .sample import sample
 
 
 def configure(ctx, param, configfile):
@@ -64,6 +67,7 @@ def main(ctx, config, tag, **args):
     del obj['quit']
 
 
+main.add_command(config)
 main.add_command(data)
 main.add_command(find)
 main.add_command(init)
@@ -74,3 +78,5 @@ def main(ctx, config, tag, **args):
 main.add_command(trial)
 main.add_command(auto)
 main.add_command(figure)
+main.add_command(mpeg)
+main.add_command(sample)

src/hotaru/console/mpeg.py

@@ -0,0 +1,17 @@
+import click
+
+from hotaru.sim.mpeg import make_mpeg
+
+
+@click.command()
+@click.option('--stage', '-s', type=int)
+@click.option('--has-truth', is_flag=True)
+@click.pass_obj
+def mpeg(obj, stage, has_truth):
+    '''Make Mp4'''
+
+    if stage is None:
+        stage = 'curr'
+    else:
+        stage = f'{stage:03}'
+    make_mpeg(obj.data_tag, obj.tag, stage, has_truth)

src/hotaru/console/sample.py

@@ -0,0 +1,27 @@
+import click
+
+from hotaru.sim.make import make_sim
+
+
+@click.command()
+@click.option('--outdir', type=click.Path(), default='sample', show_default=True)
+@click.option('--width', type=int, default=200, show_default=True)
+@click.option('--height', type=int, default=200, show_default=True)
+@click.option('--frames', type=int, default=1000, show_default=True)
+@click.option('--hz', type=float, default=20.0, show_default=True)
+@click.option('--num-neurons', type=int, default=1000, show_default=True)
+@click.option('--intensity-min', type=float, default=0.5, show_default=True)
+@click.option('--intensity-max', type=float, default=2.0, show_default=True)
+@click.option('--radius-min', type=float, default=4.0, show_default=True)
+@click.option('--radius-max', type=float, default=8.0, show_default=True)
+@click.option('--radius-min', type=float, default=4.0, show_default=True)
+@click.option('--distance', type=float, default=1.8, show_default=True)
+@click.option('--firingrate-min', type=float, default=0.2, show_default=True)
+@click.option('--firingrate-max', type=float, default=2.2, show_default=True)
+@click.option('--tau_rise', type=float, default=0.08, show_default=True)
+@click.option('--tau_fall', type=float, default=0.18, show_default=True)
+@click.option('--seed', type=int)
+def sample(**args):
+    '''Make Sample'''
+
+    make_sim(**args)

src/hotaru/sim/make.py

@@ -1,4 +1,5 @@
 import random
+import os
 
 import tensorflow as tf
 
@@ -11,11 +12,24 @@
 from hotaru.train.dynamics import SpikeToCalcium
 
 
-def make_sim(nv=1000, h=200, w=200, hz=20.0, nk=1000, sig_min=0.5, sig_max=2.0, min_dist=1.8, seed=None):
+def make_sim(
+    outdir='sample',
+    frames=1000, height=200, width=200, hz=20.0, num_neurons=1000,
+    intensity_min=0.5, intensity_max=2.0, radius_min=4.0, radius_max=8.0,
+    firingrate_min=0.2, firingrate_max=2.2, distance=1.8,
+    tau_rise=0.08, tau_fall=0.16, seed=None,
+):
+    os.makedirs(f'{outdir}/truth', exist_ok=True)
+    w, h, nv = width, height, frames
+    nk = num_neurons
+    sig_min, sig_max = intensity_min, intensity_max
+    rad_min, rad_max = radius_min, radius_max
+    fr_min, fr_max = firingrate_min, firingrate_max
+    min_dist = distance
     np.random.seed(seed)
 
     gamma = SpikeToCalcium()
-    gamma.set_double_exp(hz, 0.08, 0.16, 6.0)
+    gamma.set_double_exp(hz, tau_rise, tau_fall, 6.0)
     nu = nv + gamma.pad
 
     a_true = []
@@ -35,14 +49,14 @@ def make_sim(nv=1000, h=200, w=200, hz=20.0, nk=1000, sig_min=0.5, sig_max=2.0,
         if ylist.size  == 0:
             break
         for i in range(10):
-            radius = st.uniform(4.0, 4.0).rvs()
+            radius = st.uniform(rad_min, rad_max - rad_min).rvs()
             r = np.random.randint(ylist.size)
             y0, x0 = ylist[r], xlist[r]
             if (len(xs) == 0) or np.all((np.array(xs) - x0)**2 + (np.array(ys) - y0)**2 > (min_dist*radius)**2):
                 break
         if i == 9:
             break
-        rate = st.uniform(0.2 / hz, 2.0 / hz).rvs()
+        rate = st.uniform(fr_min / hz, (fr_max - fr_min) / hz).rvs()
         ui = st.bernoulli(rate).rvs(nu)
         signal = st.uniform(sig_min, sig_max).rvs()
         cond = (xlist - x0)**2 + (ylist - y0)**2 > (min_dist*radius)**2
@@ -75,17 +89,7 @@ def make_sim(nv=1000, h=200, w=200, hz=20.0, nk=1000, sig_min=0.5, sig_max=2.0,
     base_x = -5.0 * (((x - hh) / hh)**2 + ((y - wh) / wh)**2)
     imgs = (f_t + n_t + base_t + base_x).numpy()
 
-    np.save('./a0.npy', a_t.numpy())
-    np.save('./u0.npy', u_t.numpy())
-    np.save('./v0.npy', v_t.numpy())
-    np.save('./f0.npy', imgs)
-    tifffile.imwrite('./imgs.tif', imgs)
-
-    imgs -= imgs.mean(axis=0, keepdims=True)
-    imgs -= imgs.mean(axis=(1, 2), keepdims=True)
-    imgs /= imgs.std()
-    tifffile.imwrite('./norm.tif', imgs)
-
-
-if __name__ == '__main__':
-    make_sim(nk=100, sig_min=1.0)
+    np.save(f'{outdir}/truth/a0.npy', a_t.numpy())
+    np.save(f'{outdir}/truth/u0.npy', u_t.numpy())
+    np.save(f'{outdir}/truth/v0.npy', v_t.numpy())
+    tifffile.imwrite(f'{outdir}/imgs.tif', imgs)

src/hotaru/sim/mpeg.py

@@ -10,7 +10,8 @@
 from hotaru.util.mpeg import MpegStream
 
 
-def make_mpeg(tag='defautl', outfile='sample.mp4', stage='curr', data_tag='default'):
+def make_mpeg(data_tag, tag, stage, has_truth=False):
+    outfile = f'hotaru/figure/{tag}_{stage}.mp4'
     cmap = get_cmap('Greens')
     p = load_pickle(f'hotaru/log/{data_tag}_data.pickle')
     mask = p['mask']
@@ -25,11 +26,13 @@ def make_mpeg(tag='defautl', outfile='sample.mp4', stage='curr', data_tag='defau
     data = load_tfrecord(f'hotaru/data/{data_tag}.tfrecord')
     data = unmasked(data, mask)
 
-    a0 = load_numpy('a0.npy')
-    a0 = a0 > 0.5
-    v0 = load_numpy('v0.npy')
-    v0 -= v0.min(axis=1, keepdims=True)
-    v0 /= (smax - smin)
+    if has_truth:
+        a0 = load_numpy('truth/a0.npy')
+        a0 = a0 > 0.5
+        v0 = load_numpy('truth/v0.npy')
+        v0 -= v0.min(axis=1, keepdims=True)
+        v0 /= (smax - smin)
+        v0 *= 2.0
 
     a2 = load_numpy(f'hotaru/segment/{tag}_{stage}.npy')
     a2 = a2.reshape(-1, h, w)
@@ -41,26 +44,33 @@ def make_mpeg(tag='defautl', outfile='sample.mp4', stage='curr', data_tag='defau
         v2 = g(u2).numpy()
     v2 *= sstd / (smax - smin)
     v2 -= v2.min(axis=1, keepdims=True)
-
-    v0 *= 2.0
     v2 *= 2.0
 
-    filters = [
-        ('drawtext', dict(x=10, y=10, text='orig')),
-        ('drawtext', dict(x=10 + w, y=10, text='true')),
-        ('drawtext', dict(x=10 + 2 * w, y=10, text='HOTARU')),
-    ]
-    with MpegStream(3 * w, h, hz, outfile, filters) as mpeg:
-        for t, d in enumerate(data.as_numpy_iterator()):
-            imgo = d * sstd + avgt[t] + avgx
-            imgo = (imgo - smin) / (smax - smin)
-            img0 = np.clip((a0 * v0[:, t, None, None]).sum(axis=0), 0.0, 1.0)
-            img2 = np.clip((a2 * v2[:, t, None, None]).sum(axis=0), 0.0, 1.0)
-            img = np.concatenate([imgo, img0, img2], axis=1)
-            img = (255 * cmap(img)).astype(np.uint8)
-            mpeg.write(img)
-
-
-if __name__ == '__main__':
-    import sys
-    make_mpeg(sys.argv[1])
+    if has_truth:
+        filters = [
+            ('drawtext', dict(x=10, y=10, text='orig')),
+            ('drawtext', dict(x=10 + w, y=10, text='true')),
+            ('drawtext', dict(x=10 + 2 * w, y=10, text='HOTARU')),
+        ]
+        with MpegStream(3 * w, h, hz, outfile, filters) as mpeg:
+            for t, d in enumerate(data.as_numpy_iterator()):
+                imgo = d * sstd + avgt[t] + avgx
+                imgo = (imgo - smin) / (smax - smin)
+                img0 = np.clip((a0 * v0[:, t, None, None]).sum(axis=0), 0.0, 1.0)
+                img2 = np.clip((a2 * v2[:, t, None, None]).sum(axis=0), 0.0, 1.0)
+                img = np.concatenate([imgo, img0, img2], axis=1)
+                img = (255 * cmap(img)).astype(np.uint8)
+                mpeg.write(img)
+    else:
+        filters = [
+            ('drawtext', dict(x=10, y=10, text='orig')),
+            ('drawtext', dict(x=10 + w, y=10, text='HOTARU')),
+        ]
+        with MpegStream(2 * w, h, hz, outfile, filters) as mpeg:
+            for t, d in enumerate(data.as_numpy_iterator()):
+                imgo = d * sstd + avgt[t] + avgx
+                imgo = (imgo - smin) / (smax - smin)
+                img2 = np.clip((a2 * v2[:, t, None, None]).sum(axis=0), 0.0, 1.0)
+                img = np.concatenate([imgo, img2], axis=1)
+                img = (255 * cmap(img)).astype(np.uint8)
+                mpeg.write(img)