RF: Widespread refactorings

With the aim of making the fsl/win-pytreatxrepository independent of any specific pytreat.

Pandas talk migrated to applications/pandas/.

fslpy practical migrated to applications/fsply/.

Python introduction talk migrated to getting_started/00_overview

applications/fslpy/fslpy.ipynb

@@ -564,7 +564,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "featdir = op.join('08_fslpy', 'fmri.feat')\n",
+    "featdir = op.join('fslpy', 'fmri.feat')\n",
     "\n",
     "tstat1 = Image(op.join(featdir, 'stats', 'tstat1')).data\n",
     "\n",
@@ -725,7 +725,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "featdir = op.join(op.join('08_fslpy', 'fmri.feat'))\n",
+    "featdir = op.join(op.join('fslpy', 'fmri.feat'))\n",
     "tstat1  = Image(op.join(featdir, 'stats', 'tstat1'))\n",
     "std     = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))"
    ]
@@ -831,7 +831,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "featdir = op.join('08_fslpy', 'fmri.feat')\n",
+    "featdir = op.join('fslpy', 'fmri.feat')\n",
     "func    = Image(op.join(featdir, 'reg', 'example_func'))\n",
     "struc   = Image(op.join(featdir, 'reg', 'highres'))\n",
     "std     = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))"
@@ -1019,9 +1019,9 @@
    "source": [
     "from fsl.wrappers import robustfov\n",
     "\n",
-    "robustfov('08_fslpy/bighead', 'bighead_cropped')\n",
+    "robustfov('fslpy/bighead', 'bighead_cropped')\n",
     "\n",
-    "render('08_fslpy/bighead bighead_cropped -cm blue')"
+    "render('fslpy/bighead bighead_cropped -cm blue')"
    ]
   },
   {
@@ -1166,8 +1166,8 @@
     "from fsl.wrappers import flirt\n",
     "\n",
     "std2mm   = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))\n",
-    "tstat1   = Image(op.join('08_fslpy', 'fmri.feat', 'stats', 'tstat1'))\n",
-    "func2std = np.loadtxt(op.join('08_fslpy', 'fmri.feat', 'reg', 'example_func2standard.mat'))\n",
+    "tstat1   = Image(op.join('fslpy', 'fmri.feat', 'stats', 'tstat1'))\n",
+    "func2std = np.loadtxt(op.join('fslpy', 'fmri.feat', 'reg', 'example_func2standard.mat'))\n",
     "\n",
     "aligned = flirt(tstat1, std2mm, applyxfm=True, init=func2std, out=LOAD)\n",
     "\n",
@@ -1576,8 +1576,8 @@
     "# You can pass the command\n",
     "# and its arguments as a single\n",
     "# string, or as a sequence\n",
-    "print('Lines in this notebook:', run('wc -l 08_fslpy.md').strip())\n",
-    "print('Words in this notebook:', run(['wc', '-w', '08_fslpy.md']).strip())"
+    "print('Lines in this notebook:', run('wc -l fslpy.md').strip())\n",
+    "print('Words in this notebook:', run(['wc', '-w', 'fslpy.md']).strip())"
    ]
   },
   {
@@ -1775,7 +1775,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "jobid = bet('08_fslpy/bighead', 'bighead_brain', submit=True)\n",
+    "jobid = bet('fslpy/bighead', 'bighead_brain', submit=True)\n",
     "print('Job ID:', jobid)"
    ]
   },
@@ -1798,11 +1798,11 @@
    "outputs": [],
    "source": [
     "from fsl.utils.run import hold\n",
-    "jobid = bet('08_fslpy/bighead', 'bighead_brain', submit=True)\n",
+    "jobid = bet('fslpy/bighead', 'bighead_brain', submit=True)\n",
     "print('Job ID:', jobid)\n",
     "hold(jobid)\n",
     "print('Done!')\n",
-    "render('08_fslpy/bighead bighead_brain -cm hot')"
+    "render('fslpy/bighead bighead_brain -cm hot')"
    ]
   },
   {
@@ -1822,7 +1822,7 @@
    "outputs": [],
    "source": [
     "jobs = []\n",
-    "jobs.append(runfsl('robustfov -i 08_fslpy/bighead -r bighead_cropped',    submit=True, queue='short.q'))\n",
+    "jobs.append(runfsl('robustfov -i fslpy/bighead -r bighead_cropped',       submit=True, queue='short.q'))\n",
     "jobs.append(runfsl('bet bighead_cropped bighead_brain',                   submit=True, queue='short.q', wait_for=jobs[-1]))\n",
     "jobs.append(runfsl('fslroi bighead_brain bighead_slices 0 -1 111 3 0 -1', submit=True, queue='short.q', wait_for=jobs[-1]))\n",
     "jobs.append(runfsl('fast -o bighead_fast bighead_slices',                 submit=True, queue='short.q', wait_for=jobs[-1]))\n",
@@ -1901,8 +1901,8 @@
    "outputs": [],
    "source": [
     "with open('commands.log', 'wt') as cmdlog:\n",
-    "     run('./mycmd 0',         log={'cmd' : cmdlog})\n",
-    "     run('wc -l 08_fslpy.md', log={'cmd' : cmdlog})\n",
+    "     run('./mycmd 0',      log={'cmd' : cmdlog})\n",
+    "     run('wc -l fslpy.md', log={'cmd' : cmdlog})\n",
     "\n",
     "print('\\nCommand log:')\n",
     "!cat commands.log"